Publications des utilisateurs
2025
Fakhfakh M., Sarry L., Clarysse P. HALSR-Net: Improving CNN Segmentation of Cardiac Left Ventricle MRI with Hybrid Attention and Latent Space Reconstruction Computerized Medical Imaging and Graphics Volume 123, July 2025, 102546 DOI:10.1016/j.compmedimag.2025.102546
Debroas, D. Global analysis of the metaplasmidome: ecological drivers and spread of antibiotic resistance genes across ecosystems. Microbiome 2025 13, 77 DOI:10.1186/s40168-025-02062-5
Monjot, A., Rousseau, J., Bittner, L. et al. Metatranscriptomes-based sequence similarity networks uncover genetic signatures within parasitic freshwater microbial eukaryotes. Microbiome 2025 13, 43 DOI:10.1186/s40168-024-02027-0
Péguilhan, R., Rossi, F., Joly, M., Nasr, E., Batut, B., Enault, F., Ervens, B., and Amato, P. Clouds influence the functioning of airborne microorganisms. Biogeosciences 2025 22, 1257–1275 DOI:10.5194/bg-22-1257-2025
2024
Hecquet, L., Charmantray, F., Tittmann, K., Leogrande, C., Nauton, L., Joly, M., Arbia, G. Enzymatic Upgrading of Biomass-Derived Aldoses to Rare Deoxy Ketoses Catalyzed by Transketolase Variants. ChemSusChem e202401834 DOI:10.1002/cssc.202401834
Bazile, J., Nadaud, I., Lasserre-Zuber, P., Kitt, J., De Oliveira, R., Choulet, F., Sourdille, P. TaRECQ4 contributes to maintain both homologous and homoeologous recombination during wheat meiosis. Front Plant Sci. 2024, 14 : 1342976 DOI:10.3389/fpls.2023.1342976
Chakoory, O., Barra, V., Rochette, E. et al. DeepMPTB: a vaginal microbiome-based deep neural network as artificial intelligence strategy for efficient preterm birth prediction. Biomark Res 2024, 12, 25. DOI:10.1186/s40364-024-00557-1
Dumont, Q., Cayol, V. and Froger, J.L. Is stress modeling able to forecast intrusions and slip events at Piton de la Fournaise volcano? Earth and Planetary Science Letters 2024 vol.626, p.118494, - DOI:10.1016/j.epsl.2023.118494
Hoggan, P.E., Duchamp, N., Feschet, C., and Tarragó, M.M. Quantum Monte Carlo method modeling hydrogen production using methane at Ni(111): The adsorbed formyl to CO step Adv. Quantum Chem 2024 89 p359-371. DOI:10.1016/bs.aiq.2023.11.002
Kostrykin, L., Woller, T., Kalaš, M., Özdemir, B., Andrade Buono, R., Sun, Y., Kumar, A., Goué, N., Gruening, B., Serrano-Solano, B., Fouilloux, A. Enhancing the image analysis community in Galaxy. BioHackrXiv 2024, DOI:10.37044/osf.io/w8dsz
Sahnoune Millot M., Devémy J., Chennell P., Pinguet J., Dequidt A., Sautou V., and Malfreyt P. Leaching of plasticizers from PVC medical devices: A molecular interpretation of experimental migration data. Journal of Molecular Liquids 2024, Vol.396, 123965 DOI:10.1016/j.molliq.2024.123965
Singh, J., Gudi, S., Maughan, P.J., Liu, Z., Kolmer, J., Wang, M., Chen, X., Rouse, M.N., Lasserre-Zuber, P., Rimbert, H., Sehgal, S., Fiedler, J.D., Choulet, F., Acevedo, M., Gupta, R. and Gill, U. Genomes of Aegilops umbellulata provide new insights into unique structural variations and genetic diversity in the U-genome for wheat improvement. Plant Biotechnol. J. 2024 DOI:0.1111/pbi.14470
The Galaxy Community, The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update Nucleic Acids Res. 2024 gkae410 DOI:10.1093/nar/gkae410
Tournayre, J., Polonais, V., Wawrzyniak, I., Akossi, R.F., Parisot, N., Lerat, E., Delbac, F., Souvignet, P., Reichstadt, M., and Peyretaillade, E. MicroAnnot: A Dedicated Workflow for Accurate Microsporidian Genome Annotation. Int. J. Mol. Sci. 2024, 25, 880. DOI:10.3390/ijms25020880
2023
Ageorges V., Wawrzyniak I., Ruiz P., Bicep C., Zorgani M.A., Paxman J.J., Heras B. Henderson I.R., Leroy S., Bailly X. Sapountzis P. Peyretaillade E., and Desvaux M. Genome-Wide Analysis of Antigen 43 (Ag43) Variants: New Insights in Their Diversity, Distribution and Prevalence in Bacteria Int. J. Mol. Sci. 2023 24, 5500. DOI:10.3390/ijms24065500
Akossi R. F., Delbac F., El Alaoui H., Wawrzyniak I, and Peyretaillade E. The intracellular parasite Anncaliia algerae induces a massive miRNA down-regulation in human cells Non-coding RNA Research. 2023, 8 (3): 363-375. DOI:10.1016/j.ncrna.2023.05.003
Kwiatkowski F., Serlet L. and Stos A. Oncogenetic pedigrees: Relation between design and ability to predict mutation BioSystems 2023 225: 104841 DOI:10.1016/j.biosystems.2023.104841
Hoggan, P.E. Quantum Monte Carlo method describing supported metal catalysis: Ni(111)/alumina decomposing methane as a route to hydrogen. AQC 2023 88 p291-304. DOI:10.1016/bs.aiq.2023.01.001
Lardy, R., Ruin Q. and Veissier I. Discriminating Pathological, Reproductive or Stress Conditions in Cows Using Machine Learning on Sensor-Based Activity Data. Computers and Electronics in Agriculture 2023 204 107556. DOI:10.1016/j.compag.2022.107556.
Monjot A., Bronner G., Cruaud C., Da Silva D., Courtine D., Aury J.-M., Moné A., Vellet A., Wawrzyniak I., Gavory F., Billard H., Debroas D., and Lepère C. Functional diversity of microbial eukaryotes in a meromictic lake: Coupling between metatranscriptomic and a trait-based approach Environmental Microbiology 2023, 1-17 DOI:10.1111/1462-2920.16531
Papon N., Lasserre-Zuber P., Rimbert H., De Oliveira R., Paux E. and Choulet F. All families of transposable elements were active in the recent wheat genome evolution and polyploidy had no impact on their activity Plant Genome 2023 e20347 DOI:10.1002/tpg2.20347
Péguilhan R., Rossi F., Rué O., Joly M. and Amato P. Comparative analysis of bacterial diversity in clouds and aerosols Atmospheric Environment 2023 298: 119635. DOI:10.1016/j.atmosenv.2023.119635
Rave-Bonilla, Y. P., Jessop, D. E., Moune, S., Garbin, C., and Moretti, R. Numerical modelling of the volcanic plume dispersion from the hydrothermal system of La Soufrière de Guadeloupe. Volcanica 2023 6(2), 459–477. DOI:10.30909/vol.06.02.459477
Saadaoui M., Faize M., Bonhomme L., Benyoussef N.O., Kharrat M., Chaar H., Label P. and Venisse J.-S. Assessment of Tunisian Trichoderma Isolates on Wheat Seed Germination, Seedling Growth and Fusarium Seedling Blight Suppression Microorganisms 2023, 11, 1512. DOI:10.3390/microorganisms11061512
Souc F. Web portal to gather tools to improve metabolomic annotations through API microservices based on a cloud infrastructure. UCA Master 2 internship report dumas-04474066
2022
Adamo M, Comtet-Marre S, Buttner E, Kellner H, Luis P, Vallon L, Prego R, Hofrichter M, Girlanda M, Peyret P, Marmeisse R. Fungal dye-decolorizing peroxidase diversity: roles in either intra- or extracellular processes. Appl Microbiol Biotechnol. 2022 106:2993-3007. DOI:10.1007/s00253-022-11923-0
Aury J.M., Engelen S., Istace B., Monat C., Lasserre-Zuber P., Belser C., Cruaud C., Rimbert H., Leroy P., Arribat S., Dufau I., Bellec A., Grimbichler D., Papon N., Paux E., Ranoux M., Alberti A., Wincker P.and Choulet F. Long-read and chromosome-scale assembly of the hexaploid wheat genome achieves high resolution for research and breeding. Gigascience 2022 11 DOI:10.1093/gigascience/giac034
Chakoory O., Comtet-Marre S. and Peyret P. RiboTaxa: combined approaches for rRNA genes taxonomic resolution down to the species level from metagenomics data revealing novelties NAR Genom Bioinform 2022 4(3) DOI:10.1093/nargab/lqac070
Debroas D., Hochart C. and Galand P.E. Seasonal microbial dynamics in the ocean inferred from assembled and unassembled data: a view on the unknown biosphere. ISME COMMUN. 2022 2, 87 DOI:10.1038/s43705-022-00167-8
Dumont Q., Cayol V., Froger J-L. and Peltier A. A major destabilisation structure revealed by 22 years of satellite imagery at Piton de la Fournaise Nature Communication 2022 13: 2649 DOI:10.1038/s41467-022-30109-w
Dumont Q. Modélisation du lien entre éruptions et glissements de flancs au Piton de la Fournaise thèse de doctorat de l'Université Clermont Auvergne 2022 HALId:tel-03859171
Graindorge S, Villette C, Koechler S, Groh C, Comtet-Marre S, Mercier P, Magerand R, Peyret P, Heintz D, Schaller H, Arsene-Ploetze F. The Arabidopsis thaliana-Streptomyces Interaction Is Controlled by the Metabolic Status of the Holobiont. Int J Mol Sci. 2022 23 DOI:10.3390/ijms232112952
Hiltemann S., Rasche H., Gladman S., Hotz H.-R., Larivière D., Blankenberg D., Jagtap P. D., Wollmann T., Bretaudeau A., Goué N., Griffin T. J., Royaux C., Le Bras Y., Mehta S., Syme A., Coppens F., Droesbeke B., Soranzo N., Bacon W., Psomopoulos F., Gallardo-Alba C., Davis J., Föll M. C., Fahrner M., Doyle M. A., Serrano-Solano B., Fouilloux A., van Heusden P., Maier W., Clements D., Heyl F., Grüning B., Batut B. and the Galaxy Training Network Galaxy Training: A Powerful Framework for Teaching! bioRxiv 2022 DOI:10.1101/2022.06.02.494505
Mougeot G., Dubos T., Chausse F., Péry E., Graumann K., Tatout C., Evans D.E. and Desset S. Deep learning – promises for 3D nuclear imaging: a guide for biologists. J. Cell Sci. 2022 135 (7) DOI:10.1242/jcs.258986
Nkepsu Mbitou R. L., Goujon F., Dequidt A., Latour B., Devémy J., Blaak R., Martzel N., Emeriau-Viard C.,Tchoufag J. ,Garruchet S. , Munch E., Hauret P. and Malfreyt P. Consistent and Transferable Force Fields for Statistical Copolymer Systems at the Mesoscale Journal of Chemical Theory and Computation 2022, 6940–6951p DOI:10.1021/acs.jctc.2c00945
Olo Ndela E., Roux S., Henke C., Sczyrba A., Sime Ngando T., Varsani A., Enault F. Reekeekee- and roodoodooviruses, two different Microviridae clades constituted by the smallest DNA phages. Virus Evolution, 2022 veac123, DOI:10.1093/ve/veac123
Orselly M., Devémy J., Bouvet-Marchand A., Dequidt A., Loubat C. and Malfreyt P., Molecular interactions at the metal–liquid interfaces. The Journal of Chemical Physics 2022 156(23)DOI:10.1063/5.0095872
Pouchin P., Zoghlami R., Valarcher R., Delannoy M., Carvalho M., Belle C., Mongy M., Desset S. and Brau F. Easing batch image processing from OMERO: a new toolbox for ImageJ. F1000Res. 2022 5(11) 392. DOI:10.12688/f1000research.110385.2
Pypec M., Jouffret L., Taillefumier C. and Roy O. First series of N-alkylamino peptoid homooligomers: solution phase synthesis and conformational investigation. Beilstein J. Org. Chem. 2022 18 845–854. DOI:10.3762/bjoc.18.85
Rocher F., Alouane T., Philippe G., Martin M.-L., Label P., Langin T. and Bonhomme L. Fusarium graminearum Infection Strategy in Wheat Involves a Highly Conserved Genetic Program That Controls the Expression of a Core Effectome. International Journal of Molecular Sciences. 2022 23(3):1914 DOI:10.3390/ijms23031914
Sahnoune M., Tokhadzé N., Ech Cherif El Kettani S., Devémy J., Goujon F., Chennell P., Dequidt A., Goutaudier C., Sautou V., and Malfreyt P. Drug Interactions with Plasticized PVCs. ACS Applied Polymer Materials 2022, 4, 4538−4550 DOI:10.1021/acsapm.2c00532
Sarramia D., Claude A. , Ogereau F., Mezhoud J. and Mailhot G. CEBA: A Data Lake for Data Sharing and Environmental Monitoring. Sensors 2022, 22 (7), p.2733 DOI:10.3390/s22072733
Smittarello D., Smets B., Barrière J., Michellier C., Oth O., Shreve T., Grandin R., Theys N., Brenot H., Cayol V., Allard P., Caudron C., Chevrel O., Darchambeau F., de Buyl P., Delhaye L., Derauw D., Ganci G., Geirsson H., Kamate Kaleghetso E., Kambale Makundi J., Kambale Nguomoja I., Kasereka Mahinda C., Kervyn M., Kimanuka Ruriho C., Le Mével H., Molendijk S., Namur O., Poppe S., Schmid M., Subira J., Wauthier C., Yalire M., d’Oreye N., Kervyn F. Precursor-free eruption triggered by edifice rupture at Nyiragongo volcano. Nature 2022 vol.609, p.83-88, DOI:10.1038/s41586-022-05047-8
Teseo S., Otani S., Brinch C., Leroy S., Ruiz P., Desvaux M. Forano E., Aarestrup F.M. and Sapountzis P. A global phylogenomic and metabolic reconstruction of the large intestine bacterial community of domesticated cattle. Microbiome 2022; 10, 155 DOI:10.1186/s40168-022-01357-1
2021
Aury J.-M., Engelen S., Istace B, Monat C., Lasserre-Zuber P., Belser C., Cruaud C. Rimbert H., Leroy P., Arribat S., Dufau I., Bellec A., Grimbichler D., Papon N., Paux E., Ranoux M., Alberti A., Wincker P. and Choulet F. Long-read and chromosome-scale assembly of the hexaploid wheat genome achieves high resolution for research and breeding bioRxiv, 2021 DOI:10.1101/2021.08.24.457458
Ayouba, K., Breuillé, M. L., Grivault, C. and Le Gallo, J. The spatial dimension of the French private rental markets: Evidence from microgeographic data in 2015. Environment and Planning B: Urban Analytics and City Science 2021 48(8), 2497-2513 DOI:10.1177/2399808320977877
Barnoud A., Cayol V., Lelièvre P. G., Portal A., Labazuy P., Boivin P. and Gailler L. Robust Bayesian Joint Inversion of Gravimetric and Muographic Data for the Density Imaging of the Puy de Dôme Volcano (France). Frontiers in Earth Science, 8:575842, p. 510, 2021 DOI:10.3389/feart.2020.575842
Dumont Q., Cayol V. and Froger J-L. Mitigating bias in inversion of InSAR data resulting from radar viewing geometries. Geophysical Journal International 2021 227(1), 483-495. DOI:10.1093/gji/ggab229
Philip E. Hoggan. Quantum Monte Carlo with ground-state input to investigate platinum-doped aluminum catalyst: H2 production from adsorbed CO. Advances in Quantum Chemistry, Academic Press, 2021, ISSN 0065-3276. DOI:10.1016/bs.aiq.2021.05.011
Lardy, R., de Boyer des Roches A., Capdeville J., Bastien R., Mounier L. and Veissier I. Refinement of International Recommendations for Cubicles, Based on the Identification of Associations between Cubicle Characteristics and Dairy Cow Welfare Measures. Journal of Dairy Science, 2021 104(2), 2164-84. DOI:10.3168/jds.2019-17972
Lengagne S., Kalawoun R., Bouchon F. and Mezouar Y. Reducing pessimism in Interval Analysis using Bsplines Properties: Application to Robotics. Reliable Computing 2021 27, 63-87
Marre S., Gasc C., Forest C., Lebbaoui Y., Mosoni P. and Peyret P. Revealing microbial species diversity using sequence capture by hybridization. Microb Genom. 2021 7(12) DOI:10.1099/mgen.0.000714
Mom R., Muries B., Benoit P., Robert-Paganin J., Réty S., Venisse J.S., Padua A., Label P. and Auguin D. Voltage-gating of aquaporins, a putative conserved safety mechanism during ionic stresses. FEBS Lett., 2021, 595(1), 41-57. DOI:10.1002/1873-3468.13944
Munoz G., Dequidt, A., Martzel N., Blaak R., Goujon F., Devémy J., Garruchet S., Latour B., Munch E. and Malfreyt P. Heterogeneity Effects in Highly Cross-Linked Polymer Networks. Polymers 2020 13(5), 757. DOI:10.3390/polym13050757
Nagaraj H., Clavier G., Latour B., Dequidt A., Devémy J., Garruchet S., Goujon F., Martzel N., Blaak R., Munch E. and Malfreyt P. Strain induced crystallisation of polymers at and above the crystallisation temperature by coarse-grained simulations. AIP The Journal of Chemical Physics, 2021, 154, 234902. DOI:10.1063/5.0050562
Nauton L., Hecquet L. and Théry V. QM/MM Study of Human Transketolase: Thiamine Diphosphate Activation Mechanism and Complete Catalytic Cycle ACS Journal of Chemical Information and Modeling, 2021, 1549-9596. DOI:10.1021/acs.jcim.1c00190
Nourrisson C, Scanzi J, Brunet J, Delbac F, Dapoigny M. and Poirier P. Prokaryotic and Eukaryotic Fecal Microbiota in Irritable Bowel Syndrome Patients and Healthy Individuals Colonized With Blastocystis. Front Microbiol. 2021 17(12):713347 DOI:10.3389/fmicb.2021.713347
Péguilhan R., Besaury L., Rossi F., Enault F., Baray J.-L., Deguillaume L. and Amato P. Rainfalls sprinkle cloud bacterial diversity while scavenging biomass FEMS Microbiology Ecology, 2021, 97(11). DOI:10.1093/femsec/fiab144
Ribeiro S., Label P., Garcia D., Montoro P. and Pujade-Renaud V. Transcriptome profiling in susceptible and tolerant rubber tree clones in response to cassiicolin Cas1, a necrotrophic effector from Corynespora cassiicola. PLOS ONE, 2021, 16(7). e0254541. DOI:10.1371/journal.pone.0254541
Sahnoune M., Tokhadzé N., Devémy J., Dequidt A., Goujon F., Chennell P., Sautou V., and Malfreyt P. Understanding and Characterizing the Drug Sorption to PVC and PE Materials. ACS Applied Materials & Interfaces, 2021, 13, 16, 18594-18603 (Biological and Medical Applications of Materials and Interfaces). DOI:10.1021/acsami.1c03284
Solano Canchaya J.G., Clavier G., Garruchet S., Latour B., Martzel N., Devémy J., Goujon F., Dequidt A., Blaak R., Munch E. and Malfreyt P. Rheological properties of polymer chains at a copper oxide surface: Impact of the chain length, surface coverage, and grafted polymer shape. Phys. Rev. E 104, 024501 (2021) ; DOI:10.1103/PhysRevE.104.024501
Terzian P., Olo Ndela E., Galiez C., Lossouarn J., Pérez Bucio R.E., Mom R., Toussaint A., Petit M.-A., Enault F. PHROG: families of prokaryotic virus proteins clustered using remote homology. NAR Genom Bioinform. 2021 3(3):lqab067. DOI:10.1093/nargab/lqab067
Venisse J.-S., Õunapuu-Pikas E., Dupont M., Gousset-Dupont A., Saadaoui M., Faize M., Chen S., Chen S., Petel G., Fumanal B., Roeckel-Drevet P., Sellin A. and Label P. Genome-Wide Identification, Structure Characterization, and Expression Pattern Profiling of the Aquaporin Gene Family in Betula pendula. Int. J. Mol. Sci. 2021, 22, 7269. DOI:10.3390/ijms22147269
Zhu T., Wang L., Rimbert H., Rodriguez J.C., Deal K.R., De Oliveira R., Choulet F., Keeble‐Gagnère G., Tibbits J., Rogers J., Eversole K., Appels R., Gu Y.Q., Mascher M., Dvorak J. and Luo M.‐C. Plant J. 2021 Optical maps refine the bread wheat Triticum aestivum cv Chinese Spring genome assembly. DOI:10.1111/tpj.15289
2020
De la Higuera I., Kasun G., Torrance E.L., Pratt A.A., Maluenda A., Colombet J., Bisseux M., Ravet V., Dayaram A., Stainton D., Kraberger S., Zawar-Reza P., Goldstien S., Briskie J., White R., Gomez C., Ainley D.G., Harding J.S., Fontenele R.S., Schreck J., Ribeiro S.G., Oswald S.A., Arnold J., Enault F., Varsani A., Stedman K.M. Unveiling Crucivirus Diversity by Mining Metagenomic Data. mBio. 2020 11(5): e01410-20. DOI:10.1128/mBio.01410-20
De Oliveira, R., Rimbert, H., Balfourier, F., Kitt, J., Dynomant, E., Vrána, J., Doležel, J., Cattonaro, F., Paux, E. and Choulet, F. Structural Variations Affecting Genes and Transposable Elements of Chromosome 3B in Wheats. Frontiers in Genetics 2020 11, 891. DOI:10.3389/fgene.2020.00891
Goujon F., Martzel N., Dequidt A., Latour B., Garruchet S., Devémy J., Blaak R., Munch E. and Malfreyt P. Backbone oriented anisotropic coarse grains for efficient simulations of polymers. J. Chem. Phys. 2020 153, 214901. DOI:10.1063/5.0019945.
Jalili V., Afgan E., Gu Q., Clements D., Blankenberg D., Goecks J., Taylor J. and Nekrutenko A. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: update 2020 Nucleic Acids Research, 2020 48 (W1), W395–W402 DOI:10.1017/10.1093/nar/gkaa434
Jensen S, Brasset E, Parey E, Roest Crollius H, Sharakhov IV and Vaury C. Conserved Small Nucleotidic Elements at the Origin of Concerted piRNA Biogenesis from Genes and lncRNAs. Cells 2020 9(6) DOI:10.3390/cells9061491
Lardy, R., de Boyer des Roches A., Capdeville J., Bastien R., Mounier L. and Veissier I. New Recommendations for Self-Locking Barriers to Reduce Skin Injuries in Dairy Cows. Animal 2020 14(8), 1745-1756. DOI:10.1017/S175173112000052X
Martzel N., Dequidt A., Devémy J., Blaak R., Garruchet S., Latour B., Goujon F., Munch E. and Malfreyt P. Grain Shape Dynamics for Molecular Simulations at the Mesoscale. Adv. Theory Simul. 2020 3(9), 2513-0390. DOI:10.1002/adts.202000124.
Pereira O., Hochart C., BoeufD., Auguet J.-C., Debroas D. and Galand P.E. Seasonality of archaeal proteorhodopsin and associated Marine Group IIb ecotypes (Ca. Poseidoniales) in the North Western Mediterranean Sea. ISME J. DOI:10.1038/s41396-020-00851-4
Théodose R., Denis D., Chateau T., Frémont V. and Checchin P. R-AGNO-RPN: A LIDAR-Camera Region Deep Network for Resolution-Agnostic Detection. 2020 arXiv:2012.05740
2019
Amato, P., Besaury, L., Joly, M., Penaud, B., Deguillaume, L., and Delort A.M. Metatranscriptomic exploration of microbial functioning in clouds. Scientific Reports 2019 9:4383. DOI:10.1038/s41598-019-41032-4.
Balfourier, F., Bouchet S., Robert S., De Oliveira R., Rimbert H., Kitt J. and Choulet, F. International Wheat Genome Sequencing, C. BreedWheat, and E. Paux. Worldwide phylogeography and history of wheat genetic diversity. Science Advances, 2019 5(5): p. eaav0536. DOI:10.1126/sciadv.aav0536.
Biderre-Petit C., Taib N., Gardon H., Hochart C. and Debroas D. New insights into the pelagic microorganisms involved in the methane cycle in the meromictic Lake Pavin through metagenomics. FEMS Microbiology Ecology, 2019 95(3) fiy183 DOI:0.1093/femsec/fiy183
Debroas D., Siguret C. Viruses as key reservoirs of antibiotic resistance genes in the environment. The ISME J. 2019 13 (11), 2856–2867. DOI:0.1038/s41598-019-41032-4
Hijazi H., Monier G., Gil E., Trassoudaine A., Bougerol C., Leroux C., Castelluci D., Robert-Goumet C., Hoggan P., André Y., Goktasi N.I., LaPierre R.R. and Dubrovskii V.G. Si doping of vapor-liquid-solid GaAs nanowires: n-type or p-type?. Nano Lett., 2019. DOI:10.1021/acs.nanolett.9b01308
Kempfer K., Devémy J., Dequidt A., Couty M., and Malfreyt P. Atomistic Descriptions of the cis-1,4-Polybutadiene/Silica Interfaces. ACS Applied Polymer Materials 2019 1 (5), 969-981. DOI: 10.1021/acsapm.8b00274.
Kempfer K., Devémy J., Dequidt A., Couty M. and Malfreyt P. Development of Coarse-Grained Models for Polymers by Trajectory Matching. ACS Omega 2019 4 (3), 5955-5967. DOI:10.1021/acsomega.9b00144.
Kempfer K., Devémy J., Dequidt A., Couty M. and Malfreyt P. Realistic Coarse-Grain Model of cis-1,4-Polybutadiene: From Chemistry to Rheology. Macromolecules 2019 52 (7), 2736-2747. DOI:10.1021/acs.macromol.8b02750.
Luiz Fernando Lepre, Laure Pison, Ines Otero, Arnaud Gautier, Julien Dévemy, Pascale Husson, Agilio A. H. Pádua and Margarida Costa Gomes. Using hydrogenated and perfluorinated gases to probe the interactions and structure of fluorinated ionic liquids. Phys. Chem. Chem. Phys., 2019, 21 17, 8865-8873. DOI:10.1039/C9CP00593E
Planche C., Tridon F., Banson S., Thompson G., Monier M., Battaglia A., Wobrock W. 2019. On the realism of the rain microphysics representation of a squall line in the WRF model. Part II: Sensitivity studies on the rain Drop Size Distributions. Monthly Weather Review. DOI:10.1175/MWR-D-18-0019.1.
Valérie Polonais, Sebastian Niehus, Ivan Wawrzyniak, Adrien Franchet, Christine Gaspin, Abdel Belkorchia, Matthieu Reichstadt, Caroline Belser, Karine Labadie, Arnaud Couloux, Frédéric Delbac, Eric Peyretaillade, Dominique Ferrandon. Draft genome sequence of Tubulinosema ratisbonensis, a microsporidian species infecting the model organism Drosophila melanogaster. Microbiol Resour Announc 2019 8:e00077-19. DOI:10.1128/MRA.00077-19.
Pont Caroline, Leroy Thibault, Seidel Michael, Tondelli Alessandro, Duchemin Wandrille, Armisen David, Lang Daniel, Bustos-Korts Daniela, Goué Nadia, Balfourier François, Molnár-Láng Márta, Lage Jacob, Kilian Benjamin, Özkan Hakan, Waite Darren, Dyer Sarah, Letellier Thomas, Alaux Michael, Wheat and Barley Legacy for Breeding Improvement (WHEALBI) consortium, Russell Joanne, Keller Beat, van Eeuwijk Fred, Spannagl Manuel, Mayer Klaus F.X., Waugh Robbie, Stein Nils, Cattivelli Luigi, Haberer Georg, Charmet Gilles, Salse Jérôme. Tracing the ancestry of modern bread wheats. Nature Genetics, 2019, (51) Pages 905-911. DOI:10.1038/s41588-019-0393-z.
Rabie Saidi, Wajdi Dhifli, Mondher Maddouri, and Engelbert Mephu Nguifo. Efficiently Mining Recurrent Substructures from Protein Three-Dimensional Structure Graphs. Journal of Computational Biology. 2019 26 (6), 561-571. DOI:doi.org/10.1089/cmb.2018.0171
Rajesh O. Sharma, Philip E. Hoggan, Physisorption energy of H and H 2 on clean Pt(111) as a useful surface energy reference in Quantum Monte Carlo calculation. Advances in Quantum Chemistry, 2019 DOI:10.1016/bs.aiq.2019.04.007.
R. Shyam, L. Nauton, G. Angelici, O. Roy, C. Taillefumier, S. Faure. NCα‐gem‐dimethylated peptoid side chains: A novel approach for structural control and peptide sequence mimetics. Biopolymers, e23273.DOI:10.1002/bip.23273.
Tridon F., Planche C., Mroz K., Banson S., Battaglia A., Van Baelen J., Wobrock W. 2019. On the realism of the rain microphysics representation of a squall line in the WRF model. Part I: Evaluation with multifrequency radar Doppler spectra observations. Monthly Weather Review. DOI:10.1175/MWR-D-18-0018.1.
2018
Batut B., Gravouil K., Defois C., Hiltemann S., Brugère J.-F., Peyretaillade E. and Peyret P. ASaiM:a Galaxy-base framework to analyze microbiota data. GigaScience 2018 7, 1-7. DOI:10.1093/gigascience/giy057.
International Wheat Genome Sequencing Consortium, Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science, 2018 361(6403). DOI:10.1126/science.aar7191.
Ludovic Garnier, Julien Devémy, Christine Bonal & Patrice Malfreyt. Calculations of potential of mean force: application to ion-pairs and host–guest systems. Molecular Physics, 2018 116,15-16, 1998-2008. DOI:10.1080/00268976.2018.1442593.
Ludovic Garnier, Sabine Sarraute, Yael Israëli, Christine Bonal, and Patrice Malfreyt. Associations of Water-Soluble Macrocyclic Hosts with 4-Aminoazobenzene: Impact of pH. The Journal of Physical Chemistry, 2018 122 (50), 11953-11961. DOI:10.1021/acs.jpcb.8b09127.
Hoggan P.E. Chapter Fifteen - Quantum Monte Carlo Calculations for Industrial Catalysts: Accurately Evaluating the H2 Dissociation Reaction Barrier on Pt(111). Advances in Quantum Chemistry, 2018 76, 271-278. DOI:10.1016/bs.aiq.2017.07.002).
Romain Jouve, Vincent Thery, Sylvie Ducki, Julie Helfenbein, Jean-Christophe Thiery, Aurélie Job, Elodie Picard, Christophe Mallet, Isabelle Ripoche, Khalil Bennis. Optimization of the synthesis of a key intermediate for the preparation ofglucocorticoids, Steroids, 2018 137, 14-2. DOI:10.1016/j.steroids.2018.06.007.
Kalawoun R. and S. Lengagne and F. Bouchon and Y. Mezouar. BSplines properties with Interval Analysis for Constraint Satisfaction Problem: Application in robotics. 15th International Conference on Intelligent Autonomous Systems IAS-15, Baden-Baden, Germany, June 2018.
Loiseau C., Hatte V., Andrieu C., Barlet L., Cologne A., De Oliveira R., Ferrato-Berberian L., Gardon H., Lauber D., Molinier M., Monnerie S., N 'Gou K., Penaud B., Pereira O., Picarle J., Septier A., Mahul A., Charvy J.-C. and Enault F. 2018. J. Bioinformatics, Computational and Systems Biology. arXiv:1805.05597
Lopez D., Ribeiro S., Label P., Fumanal B., Venisse J.S., Kohler A., de Oliveira R.R., Labutti K., Lipzen A., Lail K., Bauer D., Ohm R., Barry K.W., Spatafora J.W., Grigoriev I., Martin F., Pujade-Renaud V. Genome-wide analysis of Corynespora cassiicola leaf fall disease putative effectors. Frontiers in Microbiology 2018 9 : 21 DOI:10.3389/fmicb.2018.00276
Rimbert, H., B. Darrier, J. Navarro, J. Kitt, F. Choulet, M. Leveugle, J. Duarte, N. Riviere, K. Eversole, C. International Wheat Genome Sequencing, J. Le Gouis, C. on behalf The BreedWheat, A. Davassi, F. Balfourier, M.C. Le Paslier, A. Berard, D. Brunel, C. Feuillet, C. Poncet, P. Sourdille, and E. Paux, High throughput SNP discovery and genotyping in hexaploid wheat. PLoS One, 2018. 13(1): p. e0186329. DOI:10.1371/journal.pone.0186329.
Wicker, T., H. Gundlach, M. Spannagl, C. Uauy, P. Borrill, R.H. Ramirez-Gonzalez, R. De Oliveira, C. International Wheat Genome Sequencing, K.F.X. Mayer, E. Paux, and F. Choulet, Impact of transposable elements on genome structure and evolution in bread wheat. Genome Biol, 2018 19(1) p. 103. DOI:10.1186/s13059-018-1479-0.
2017
Amato Pierre, Joly Muriel, Besaury Ludovic, Oudart Anne, Taib Najwa, Moné Anne I., Deguillaume Laurent, Delort Anne-Marie and Debroas Didier. Active microorganisms thrive among extremely diverse communities in cloud water. PLoS One, 2017 12(8) e0182869. DOI:10.1371/journal.pone.0182869.
Chalhoub Gérard, Tall Hamadoun, Wang Jinpeng and Misson Michel. DFTR: Dynamic Fault-Tolerant Routing protocol for convergecast WSNs. To appear in the IEEE 86th Vehicular Technology Conference, 2017, Toronto, Canada.
K. Fauché, L Nauton, L Jouffret, F Cisnetti, A Gautier. A catalytic intramolecular nitrene insertion into a copper (i)–N-heterocyclic carbene bond yielding fused nitrogen heterocycles. Chemical Communications 53 (15), 2017, 2402-2405. DOI:10.1039/C6CC09160A.
Gasc C, Constantin A, Jaziri F, Peyret P. OCaPPI-Db: an oligonucleotide probe database for pathogen identification through hybridization capture. Database (Oxford) 2017.
T. Hjelmgaard, L Nauton, F De Riccardis, L Jouffret, S Faure. Topologically Diverse Shapes Accessible by Modular Design of Arylopeptoid Macrocycles. Organic letters 20 (1), 12/2017, 268-271. DOI:10.1021/acs.orglett.7b03660.
Hoggan Philip E. Solid surface Quantum Monte Carlo : Industrial metal catalysts. Slovak Academy of Science, Bratislava, 2017, 20-22.
Kempfer Kevin. Towards the development of realistic coarse-grained models for the description of the polymer-silica interaction. Prix Poster. EPF (European Polymer Federation), 2017, Lyon France.
Luo M-C, QG Yong, Puiu D, Wang Hao, Twardziok SO, Deal KR, Huo N, Zhu T, Wang L, Wang Y, McGuire PE, Liu S, Long H, Ramasamy RK, Rodriguez JC, Van SL, Yuan L, Wang Z, Xia Z, Xiao L, Anderson OD, Ouyang S, Liang Y, Zimin AV, Pertea G, Qi P, Bennetzen JL, Dai X, Dawson MW , Müller H-G, Kugler K, Rivarola-Duarte L, Spannagl M, Mayer KFX, Lu F-H, Bevan MW, Leroy P, Li P, You FM, Sun Q, Liu Z, Lyons E, Wicker T, Salzberg SL, Devos KM, Dvořák J. Genome sequence of the progenitor of the wheat D genome Aegilops tauschii. Nature, 23 November 2017, 551:498-502 PMID: 29143815. DOI:10.1038/nature24486
Mehdi H., Monier G., Hoggan, P. E., Bideux L., Robert-Goumet C., Dubrovskii V. G. Combined angle-resolved X-ray photoelectron spectroscopy, density functional theory and kinetic study of nitridation of gallium arsenide. Applied Surface Science, Volume 427, Part A, 2018, Pages 662-669. DOI:10.1016/j.apsusc.2017.08.002.
Tall Hamadoun, Chalhoub Gérard, Hakem Nadir and Misson Michel. Load balancing routing with queue overflow prediction for WSNs. Wireless Networks journal, 2017, 1-11. DOI:10.1007/s11276-017-1554-6.
Tall Hamadoun, Chalhoub Gérard. ABORt: Acknowledgement-Based Opportunistic Routing Protocol for High Data Rate Multichannel WSNs. Journal of Sensor and Actuator Networks, 2017 6(4) 23. DOI:10.3390/jsan6040023.
Tall Hamadoun, Chalhoub Gérard and Misson Michel. M-CoLBA: Multichannel Collaborative Load Balancing Algorithm with queue overflow avoidance in WSNs. In the 13th IEEE International Wireless Communications and Mobile Computing conference, 2017, Valencia, Spain. Pages 2127-2133.
Agílio A. H. Pádua. Resolving dispersion and induction components for polarisable molecular simulations of ionic liquids. The Journal of Chemical Physics 146, 204501, 2017. DOI:10.1063/1.4983687.
Wang Jinpeng, Chalhoub Gérard, Tall Hamadoun and Misson Michel. Routing protocol enhancement for mobility support in wireless sensor networks. In the 16th International Conference on Ad Hoc Networks and Wireless, 2017, Pages 262-275, Messina, Italy.
2016
Absi Noureddine, Hoggan Philip E. Quantum Monte Carlo investigation of two catalytic reaction paths for hydrogen synthesis on Pt(111). Recent progress in Quantum Monte Carlo, ed. S.Tanaka, L. Mitas, P-O Roy, ASC books, Symposium Series (Pacifichem), 2016, Chapter 5, Pages 77–88. DOI:10.1021/bk-2016-1234.ch005.
Parisot Nicolas, Peyretaillade Eric, Dugat-Bony Eric, Denonfoux Jeremy, Mahul Antoine, Peyret Pierre. Probe Design Strategies for Oligonucleotide Microarrays. Methods in Molecular Biology, Volume 1368, 2016, Pages 67-82. DOI:10.1007/978-1-4939-3136-1_6.
Tall Hamadoun, Chalhoub Gérard and Misson Michel. Implementation and performance evaluation of IEEE 802.15.4 unslotted CSMA/CA protocol on Contiki OS. In Annals of Telecommunications, 2016, Pages 1-10. DOI:10.1007/s12243-016-0522-y.
2015
Passerat-Palmbach Jonathan, Mazel Claude, Mahul Antoine, Hill David. Reliable Initialization of GPU-enabled Parallel Stochastic Simulations Using Mersenne Twister for Graphics Processors, European Simulation and Modelling, 2015, Essen, Belgium. Pages 187 – 195.
2014
Feria-Gervasio David, Tottey William, Gaci Nadia, Alric Monique, Cardot Michel, Peyret Pierre, Martin Jean-François, Pujos Estelle, Sébédio Jean-Louis, Brugère Jean-François. Three-stage continuous culture system with a self-generated anaerobia to study the regionalized metabolism of the human gut microbiota. J. Microbiological Meth. 2014, Vol. 96, pp 111-118. DOI:10.1016/j.mimet.2013.11.015
Roux Simon, Tournayre Jérémy, Mahul Antoine, Debroas Didier, Enault François. Metavir 2: new tools for viral metagenome comparison and assembled virome analysis. BMC Bioinformatics. 2014 15 DOI:10.1186/1471-2105-15-76
2013
Dufourt Jérémy, Pouchin Pierre, Peyret Pierre, Brasset Emilie and Vaury Chantal. NucBase, an esay to use read mapper for small RNAs. Mobile DNA. 2013. Vol 4 DOI:10.1186/1759-8753-4-1
Jaziri Faouzi, Parisot Nicolas, Abid Anis, Denonfoux Jérémie, Ribière Céline, Gasc Cyrielle, Boucher Delphine, Brugère Jean-François, Mahul Antoine, Hill David R.C., Peyretaillade Eric and Peyret Pierre. PhylODb: a 16S rRNA oligonucleotide probe database for prokaryotic identification, Oxford Database, 2013, Vol 2014 DOI:10.1093/database/bau036
Tottey William, Denonfoux Jérémie, Jaziri Faouzi, Parisot Nicolas, Missaoui Mohiedine, Hill David R.C., Borrel Guillaume, Peyretaillade Eric, Alric Monique, Harris Hugh M.B., Jeffery Ian B., Claesson Marcus J., O'Toole Paul W., Peyret Pierre, Brugère Jean-François. The Human Gut Chip “HuGChip”, an Explorative Phylogenetic Microarray for Determining Gut Microbiome Diversity at Family Level. PLoS One. 8, e62544. DOI:10.1371/journal.pone.0062544
Vincent Jonathan, Dai Zhanwu, Ravel Catherine, Choulet Frédéric, Mouzeyar Said, Bouzidi Fouad, Agier Marie, Martre Pierre. 2013, dbWFA: a web-based database for functional annotation of Triticum aestivum transcripts. Databases. Vol.13 DOI:10.1093/database/bat014