This list includes publications for which the GenoToul Bioinformatics facility has been used (hardware infrastructure / Funding / Staff members). All Sigenae’s publications have used the GenoToul Bioinformatics hardware infrastructure.

Kusch, S.; Ibrahim, H. M. M.; Zanchetta, C.; Lopez-Roques, C.; Donnadieu, C.; Raffaele, S. A Chromosome-Scale Genome Assembly Resource for Myriosclerotinia Sulcatula Infecting Sedge Grass ( Carex Sp.). MPMI 2020, 33 (7), 880–883. https://doi.org/10.1094/MPMI-03-20-0060-A.
Rasplus, J.-Y.; Blaimer, B. B.; Brady, S. G.; Burks, R. A.; Delvare, G.; Fisher, N.; Gates, M.; Gauthier, N.; Gumovsky, A. V.; Hansson, C.; Heraty, J. M.; Fusu, L.; Nidelet, S.; Pereira, R. A. S.; Sauné, L.; Ubaidillah, R.; Cruaud, A. A First Phylogenomic Hypothesis for Eulophidae (Hymenoptera, Chalcidoidea). null 2020, 54 (9–12), 597–609. https://doi.org/10.1080/00222933.2020.1762941.
Boyrie, L.; Moreau, C.; Frugier, F.; Jacquet, C.; Bonhomme, M. A Linkage Disequilibrium-Based Statistical Test for Genome-Wide Epistatic Selection Scans in Structured Populations. Heredity 2020. https://doi.org/10.1038/s41437-020-0349-1.
Donald, J.; Roy, M.; Suescun, U.; Iribar, A.; Manzi, S.; Péllissier, L.; Gaucher, P.; Chave, J. A Test of Community Assembly Rules Using Foliar Endophytes from a Tropical Forest Canopy. J Ecol 2020, 108 (4), 1605–1616. https://doi.org/10.1111/1365-2745.13344.
Milon, N.; Fuentes Rojas, J.-L.; Castinel, A.; Bigot, L.; Bouwmans, G.; Baudelle, K.; Boutonnet, A.; Gibert, A.; Bouchez, O.; Donnadieu, C.; Ginot, F.; Bancaud, A. A Tunable Filter for High Molecular Weight DNA Selection and Linked-Read Sequencing. Lab Chip 2020, 20 (1), 175–184. https://doi.org/10.1039/C9LC00965E.
Olazcuaga, L.; Loiseau, A.; Parrinello, H.; Paris, M.; Fraimout, A.; Guedot, C.; Diepenbrock, L. M.; Kenis, M.; Zhang, J.; Chen, X.; Borowiec, N.; Facon, B.; Vogt, H.; Price, D. K.; Vogel, H.; Prud’homme, B.; Estoup, A.; Gautier, M. A Whole-Genome Scan for Association with Invasion Success in the Fruit Fly Drosophila Suzukii Using Contrasts of Allele Frequencies Corrected for Population Structure. Molecular Biology and Evolution 2020, 37 (8), 2369–2385. https://doi.org/10.1093/molbev/msaa098.
Leroy, T.; Louvet, J.; Lalanne, C.; Le Provost, G.; Labadie, K.; Aury, J.; Delzon, S.; Plomion, C.; Kremer, A. Adaptive Introgression as a Driver of Local Adaptation to Climate in European White Oaks. New Phytol 2020, 226 (4), 1171–1182. https://doi.org/10.1111/nph.16095.
Radhakrishnan, G. V.; Keller, J.; Rich, M. K.; Vernié, T.; Mbadinga Mbadinga, D. L.; Vigneron, N.; Cottret, L.; Clemente, H. S.; Libourel, C.; Cheema, J.; Linde, A.-M.; Eklund, D. M.; Cheng, S.; Wong, G. K. S.; Lagercrantz, U.; Li, F.-W.; Oldroyd, G. E. D.; Delaux, P.-M. An Ancestral Signalling Pathway Is Conserved in Intracellular Symbioses-Forming Plant Lineages. Nature Plants 2020, 6 (3), 280–289. https://doi.org/10.1038/s41477-020-0613-7.
Dutech, C.; Feau, N.; Lesur, I.; Ehrenmann, F.; Letellier, T.; Li, B.; Mouden, C.; Guichoux, E.; Desprez-Loustau, M. L.; Gross, A. An Easy and Robust Method for Isolation and Validation of Single-Nucleotide Polymorphic Markers from a First Erysiphe Alphitoides Draft Genome. Mycol Progress 2020, 19 (6), 615–628. https://doi.org/10.1007/s11557-020-01580-w.
Jehl, F.; Muret, K.; Bernard, M.; Boutin, M.; Lagoutte, L.; Désert, C.; Dehais, P.; Esquerré, D.; Acloque, H.; Giuffra, E.; Djebali, S.; Foissac, S.; Derrien, T.; Pitel, F.; Zerjal, T.; Klopp, C.; Lagarrigue, S. An Integrative Atlas of Chicken Long Non-Coding Genes and Their Annotations across 25 Tissues. Sci Rep 2020, 10 (1), 20457. https://doi.org/10.1038/s41598-020-77586-x.
Dardaillon, J.; Dauga, D.; Simion, P.; Faure, E.; Onuma, T. A.; DeBiasse, M. B.; Louis, A.; Nitta, K. R.; Naville, M.; Besnardeau, L.; Reeves, W.; Wang, K.; Fagotto, M.; Guéroult-Bellone, M.; Fujiwara, S.; Dumollard, R.; Veeman, M.; Volff, J.-N.; Roest Crollius, H.; Douzery, E.; Ryan, J. F.; Davidson, B.; Nishida, H.; Dantec, C.; Lemaire, P. ANISEED 2019: 4D Exploration of Genetic Data for an Extended Range of Tunicates. Nucleic Acids Research 2020, 48 (D1), D668–D675. https://doi.org/10.1093/nar/gkz955.
Randriamihamison, N.; Vialaneix, N.; Neuvial, P. Applicability and Interpretability of Ward’s Hierarchical Agglomerative Clustering With or Without Contiguity Constraints. Journal of Classification 2020. https://doi.org/10.1007/s00357-020-09377-y.
Chambers, E. A.; Hebert, P. D. N. Assessing DNA Barcodes for Species Identification in North American Reptiles and Amphibians in Natural History Collections. PLoS One 2016, 11 (4), e0154363. https://doi.org/10.1371/journal.pone.0154363.
Reverter, A.; Vitezica, Z. G.; Naval-Sánchez, M.; Henshall, J.; Raidan, F. S. S.; Li, Y.; Meyer, K.; Hudson, N. J.; Porto-Neto, L. R.; Legarra, A. Association Analysis of Loci Implied in “Buffering” Epistasis. Journal of Animal Science 2020, 98 (skaa045). https://doi.org/10.1093/jas/skaa045.
Macedo, F. L.; Reverter, A.; Legarra, A. Behavior of the Linear Regression Method to Estimate Bias and Accuracies with Correct and Incorrect Genetic Evaluation Models. Journal of Dairy Science 2020, 103 (1), 529–544. https://doi.org/10.3168/jds.2019-16603.
Macedo, F. L.; Christensen, O. F.; Astruc, J.-M.; Aguilar, I.; Masuda, Y.; Legarra, A. Bias and Accuracy of Dairy Sheep Evaluations Using BLUP and SSGBLUP with Metafounders and Unknown Parent Groups. Genetics Selection Evolution 2020, 52 (1), 47. https://doi.org/10.1186/s12711-020-00567-1.
Joulian, C.; Fonti, V.; Chapron, S.; Bryan, C. G.; Guezennec, A.-G. Bioleaching of Pyritic Coal Wastes: Bioprospecting and Efficiency of Selected Consortia. Research in Microbiology 2020, 171 (7), 260–270. https://doi.org/10.1016/j.resmic.2020.08.002.
Mat, A. M.; Sarrazin, J.; Markov, G. V.; Apremont, V.; Dubreuil, C.; Eché, C.; Fabioux, C.; Klopp, C.; Sarradin, P.-M.; Tanguy, A.; Huvet, A.; Matabos, M. Biological Rhythms in the Deep-Sea Hydrothermal Mussel Bathymodiolus Azoricus. Nat Commun 2020, 11 (1), 3454. https://doi.org/10.1038/s41467-020-17284-4.
Feron, R.; Zahm, M.; Cabau, C.; Klopp, C.; Roques, C.; Bouchez, O.; Eché, C.; Valière, S.; Donnadieu, C.; Haffray, P.; Bestin, A.; Morvezen, R.; Acloque, H.; Euclide, P. T.; Wen, M.; Jouano, E.; Schartl, M.; Postlethwait, J. H.; Schraidt, C.; Christie, M. R.; Larson, W. A.; Herpin, A.; Guiguen, Y. Characterization of a Y‐specific Duplication/Insertion of the Anti‐Mullerian Hormone Type II Receptor Gene Based on a Chromosome‐scale Genome Assembly of Yellow Perch, Perca Flavescens. Mol Ecol Resour 2020, 20 (2), 531–543. https://doi.org/10.1111/1755-0998.13133.
Miyauchi, S.; Hage, H.; Drula, E.; Lesage-Meessen, L.; Berrin, J.-G.; Navarro, D.; Favel, A.; Chaduli, D.; Grisel, S.; Haon, M.; Piumi, F.; Levasseur, A.; Lomascolo, A.; Ahrendt, S.; Barry, K.; LaButti, K. M.; Chevret, D.; Daum, C.; Mariette, J.; Klopp, C.; Cullen, D.; de Vries, R. P.; Gathman, A. C.; Hainaut, M.; Henrissat, B.; Hildén, K. S.; Kües, U.; Lilly, W.; Lipzen, A.; Mäkelä, M. R.; Martinez, A. T.; Morel-Rouhier, M.; Morin, E.; Pangilinan, J.; Ram, A. F. J.; Wösten, H. A. B.; Ruiz-Dueñas, F. J.; Riley, R.; Record, E.; Grigoriev, I. V.; Rosso, M.-N. Conserved White-Rot Enzymatic Mechanism for Wood Decay in the Basidiomycota Genus Pycnoporus. DNA Research 2020, 27 (2), dsaa011. https://doi.org/10.1093/dnares/dsaa011.
Policarpo, M.; Fumey, J.; Lafargeas, P.; Naquin, D.; Thermes, C.; Naville, M.; Dechaud, C.; Volff, J.-N.; Cabau, C.; Klopp, C.; Møller, P. R.; Bernatchez, L.; García-Machado, E.; Rétaux, S.; Casane, D. Contrasting Gene Decay in Subterranean Vertebrates: Insights from Cavefishes and Fossorial Mammals. Molecular Biology and Evolution 2020, msaa249. https://doi.org/10.1093/molbev/msaa249.
Mussard, E.; Pouzet, C.; Helies, V.; Pascal, G.; Fourre, S.; Cherbuy, C.; Rubio, A.; Vergnolle, N.; Combes, S.; Beaumont, M. Culture of Rabbit Caecum Organoids by Reconstituting the Intestinal Stem Cell Niche in Vitro with Pharmacological Inhibitors or L-WRN Conditioned Medium. Stem Cell Research 2020, 48, 101980. https://doi.org/10.1016/j.scr.2020.101980.
Payton, L.; Noirot, C.; Hoede, C.; Hüppe, L.; Last, K.; Wilcockson, D.; Ershova, E. A.; Valière, S.; Meyer, B. Daily Transcriptomes of the Copepod Calanus Finmarchicus during the Summer Solstice at High Arctic Latitudes. Scientific Data 2020, 7 (1), 415. https://doi.org/10.1038/s41597-020-00751-4.
Rougemont, Q.; Moore, J.-S.; Leroy, T.; Normandeau, E.; Rondeau, E. B.; Withler, R. E.; Van Doornik, D. M.; Crane, P. A.; Naish, K. A.; Garza, J. C.; Beacham, T. D.; Koop, B. F.; Bernatchez, L. Demographic History Shaped Geographical Patterns of Deleterious Mutation Load in a Broadly Distributed Pacific Salmon. PLoS Genet 2020, 16 (8), e1008348. https://doi.org/10.1371/journal.pgen.1008348.
mariadassou, M.; Ramayo‐Caldas, Y.; Charles, M.; Féménia, M.; Renand, G.; Rocha, D. Detection of Selection Signatures in Limousin Cattle Using Whole‐genome Resequencing. Anim Genet 2020, 51 (5), 815–819. https://doi.org/10.1111/age.12982.
Teyssier, A.; Matthysen, E.; Hudin, N. S.; de Neve, L.; White, J.; Lens, L. Diet Contributes to Urban-Induced Alterations in Gut Microbiota: Experimental Evidence from a Wild Passerine. Proceedings of the Royal Society B: Biological Sciences 2020, 287 (1920), 20192182. https://doi.org/10.1098/rspb.2019.2182.
Grimm, P.; Combes, S.; Pascal, G.; Cauquil, L.; Julliand, V. Dietary Composition and Yeast/Microalgae Combination Supplementation Modulate the Microbial Ecosystem in the Caecum, Colon and Faeces of Horses. British Journal of Nutrition 2020, 123 (4), 372–382. https://doi.org/10.1017/S0007114519002824.
Sow, A.; Haran, J.; Benoit, L.; Galan, M.; Brévault, T. DNA Metabarcoding as a Tool for Disentangling Food Webs in Agroecosystems. Insects 2020, 11 (5), 294. https://doi.org/10.3390/insects11050294.
Żarski, D.; Le Cam, A.; Nynca, J.; Klopp, C.; Ciesielski, S.; Sarosiek, B.; Montfort, J.; Król, J.; Fontaine, P.; Ciereszko, A.; Bobe, J. Domestication Modulates the Expression of Genes Involved in Neurogenesis in High‐quality Eggs of Sander Lucioperca. Mol Reprod Dev 2020, 87 (9), 934–951. https://doi.org/10.1002/mrd.23414.
Paës, C.; Gidenne, T.; Bébin, K.; Duperray, J.; Gohier, C.; Guené-Grand, E.; Rebours, G.; Bouchez, O.; Barilly, C.; Aymard, P.; Combes, S. Early Introduction of Solid Feeds: Ingestion Level Matters More Than Prebiotic Supplementation for Shaping Gut Microbiota. Frontiers in Veterinary Science 2020, 7, 261. https://doi.org/10.3389/fvets.2020.00261.
Garcia-Baccino, C. A.; Lourenco, D. A. L.; Miller, S.; Cantet, R. J. C.; Vitezica, Z. G. Estimating Dominance Genetic Variances for Growth Traits in American Angus Males Using Genomic Models. Journal of Animal Science 2020, 98 (1), skz384. https://doi.org/10.1093/jas/skz384.
Jallet, A. J.; Le Rouzic, A.; Genissel, A. Evolution and Plasticity of the Transcriptome Under Temperature Fluctuations in the Fungal Plant Pathogen Zymoseptoria Tritici. Frontiers in Microbiology 2020, 11, 2180. https://doi.org/10.3389/fmicb.2020.573829.
Baksay, S.; Pornon, A.; Burrus, M.; Mariette, J.; Andalo, C.; Escaravage, N. Experimental Quantification of Pollen with DNA Metabarcoding Using ITS1 and TrnL. Scientific Reports 2020, 10 (1), 4202. https://doi.org/10.1038/s41598-020-61198-6.
Rasplus, J.; Rodriguez, L. J.; Sauné, L.; Peng, Y.; Bain, A.; Kjellberg, F.; Harrison, R. D.; Pereira, R. A. S.; Ubaidillah, R.; Tollon‐Cordet, C.; Gautier, M.; Rossi, J.; Cruaud, A. Exploring Systematic Biases, Rooting Methods and Morphological Evidence to Unravel the Evolutionary History of the Genus Ficus (Moraceae). Cladistics 2020, cla.12443. https://doi.org/10.1111/cla.12443.
Granado-Tajada, I.; Legarra, A.; Ugarte, E. Exploring the Inclusion of Genomic Information and Metafounders in Latxa Dairy Sheep Genetic Evaluations. Journal of Dairy Science 2020, 103 (7), 6346–6353. https://doi.org/10.3168/jds.2019-18033.
Magro, A.; Lecompte, E.; Hemptinne, J.-L.; Soares, A. O.; Dutrillaux, A.-M.; Murienne, J.; Fürsch, H.; Dutrillaux, B. First Case of Parthenogenesis in Ladybirds (Coleoptera: Coccinellidae) Suggests New Mechanisms for the Evolution of Asexual Reproduction. Journal of Zoological Systematics and Evolutionary Research 2020, 58 (1), 194–208. https://doi.org/10.1111/jzs.12339.
Chateigner, A.; Lesage-Descauses, M.-C.; Rogier, O.; Jorge, V.; Leplé, J.-C.; Brunaud, V.; Roux, C. P.-L.; Soubigou-Taconnat, L.; Martin-Magniette, M.-L.; Sanchez, L.; Segura, V. Gene Expression Predictions and Networks in Natural Populations Supports the Omnigenic Theory. BMC Genomics 2020, 21 (1), 416. https://doi.org/10.1186/s12864-020-06809-2.
Goñi-Urriza, M.; Klopp, C.; Ranchou-Peyruse, M.; Ranchou-Peyruse, A.; Monperrus, M.; Khalfaoui-Hassani, B.; Guyoneaud, R. Genome Insights of Mercury Methylation among Desulfovibrio and Pseudodesulfovibrio Strains. Research in Microbiology 2020, 171 (1), 3–12. https://doi.org/10.1016/j.resmic.2019.10.003.
Takehana, Y.; Zahm, M.; Cabau, C.; Klopp, C.; Roques, C.; Bouchez, O.; Donnadieu, C.; Barrachina, C.; Journot, L.; Kawaguchi, M.; Yasumasu, S.; Ansai, S.; Naruse, K.; Inoue, K.; Shinzato, C.; Schartl, M.; Guiguen, Y.; Herpin, A. Genome Sequence of the Euryhaline Javafish Medaka, Oryzias Javanicus : A Small Aquarium Fish Model for Studies on Adaptation to Salinity. G3 2020, 10 (3), 907–915. https://doi.org/10.1534/g3.119.400725.
Phan, N. T.; Orjuela, J.; Danchin, E. G. J.; Klopp, C.; Perfus‐Barbeoch, L.; Kozlowski, D. K.; Koutsovoulos, G. D.; Lopez‐Roques, C.; Bouchez, O.; Zahm, M.; Besnard, G.; Bellafiore, S. Genome Structure and Content of the Rice Root‐knot Nematode ( Meloidogyne Graminicola ). Ecol Evol 2020, 10 (20), 11006–11021. https://doi.org/10.1002/ece3.6680.
Talouarn, E.; Bardou, P.; Palhière, I.; Oget, C.; Clément, V.; Tosser-Klopp, G.; Rupp, R.; Robert-Granié, C.; The VarGoats Consortium. Genome Wide Association Analysis on Semen Volume and Milk Yield Using Different Strategies of Imputation to Whole Genome Sequence in French Dairy Goats. BMC Genetics 2020, 21 (1), 19. https://doi.org/10.1186/s12863-020-0826-9.
Ibrahim, H. M. M.; Kusch, S.; Didelon, M.; Raffaele, S. Genome‐wide Alternative Splicing Profiling in the Fungal Plant Pathogen Sclerotinia Sclerotiorum during the Colonization of Diverse Host Families. Mol Plant Pathol 2020, mpp.13006. https://doi.org/10.1111/mpp.13006.
Willemsen, A.; van den Boom, A.; Dietz, J.; Bilge Dagalp, S.; Dogan, F.; Bravo, I. G.; Ehrhardt, A.; Ehrke-Schulz, E. Genomic and Phylogenetic Characterization of ChPV2, a Novel Goat PV Closely Related to the Xi-PV1 Species Infecting Bovines. Virol J 2020, 17 (1), 167. https://doi.org/10.1186/s12985-020-01440-9.
Salem, E.; Dhanasekaran, V.; Cassard, H.; Hause, B.; Maman, S.; Meyer, G.; Ducatez, M. F. Global Transmission, Spatial Segregation, and Recombination Determine the Long-Term Evolution and Epidemiology of Bovine Coronaviruses. Viruses 2020, 12 (5), 534. https://doi.org/10.3390/v12050534.
Beaumont, M.; Paës, C.; Mussard, E.; Knudsen, C.; Cauquil, L.; Aymard, P.; Barilly, C.; Gabinaud, B.; Zemb, O.; Fourre, S.; Gautier, R.; Lencina, C.; Eutamène, H.; Theodorou, V.; Canlet, C.; Combes, S. Gut Microbiota Derived Metabolites Contribute to Intestinal Barrier Maturation at the Suckling-to-Weaning Transition. null 2020, 11 (5), 1268–1286. https://doi.org/10.1080/19490976.2020.1747335.
Graux, A.-I.; Resmond, R.; Casellas, E.; Delaby, L.; Faverdin, P.; Le Bas, C.; Ripoche, D.; Ruget, F.; Thérond, O.; Vertès, F.; Peyraud, J.-L. High-Resolution Assessment of French Grassland Dry Matter and Nitrogen Yields. European Journal of Agronomy 2020, 112, 125952. https://doi.org/10.1016/j.eja.2019.125952.
Dussert, Y.; Legrand, L.; Mazet, I. D.; Couture, C.; Piron, M.-C.; Serre, R.-F.; Bouchez, O.; Mestre, P.; Toffolatti, S. L.; Giraud, T.; Delmotte, F. Identification of the First Oomycete Mating-Type Locus Sequence in the Grapevine Downy Mildew Pathogen, Plasmopara Viticola. Current Biology 2020, 30 (20), 3897-3907.e4. https://doi.org/10.1016/j.cub.2020.07.057.
Lorenzi, C.; Barriere, S.; Villemin, J.-P.; Dejardin Bretones, L.; Mancheron, A.; Ritchie, W. IMOKA: K-Mer Based Software to Analyze Large Collections of Sequencing Data. Genome Biol 2020, 21 (1), 261. https://doi.org/10.1186/s13059-020-02165-2.
Boulesnane, Y.; Leloup, J.; Lerch, T. Z.; Roynette, A.; Pensé-Lhéritier, A.-M.; Mielcarek, C.; Changey, F. Impact of Sampling and DNA Extraction Methods on Skin Microbiota Assessment. Journal of Microbiological Methods 2020, 171, 105880. https://doi.org/10.1016/j.mimet.2020.105880.
Tournayre, O.; Leuchtmann, M.; Filippi-Codaccioni, O.; Trillat, M.; Piry, S.; Pontier, D.; Charbonnel, N.; Galan, M. In Silico and Empirical Evaluation of Twelve Metabarcoding Primer Sets for Insectivorous Diet Analyses. Ecology and Evolution 2020, 10 (13), 6310–6332. https://doi.org/10.1002/ece3.6362.
Robic, A.; Demars, J.; Kühn, C. In-Depth Analysis Reveals Production of Circular RNAs from Non-Coding Sequences. Cells 2020, 9 (8), 1806. https://doi.org/10.3390/cells9081806.
Ploypetch, S.; Roytrakul, S.; Phaonakrop, N.; Kittisenachai, S.; Leetanasaksakul, K.; Pisamai, S.; Kalpravidh, C.; Rungsipipat, A.; Suriyaphol, G. In-Gel Digestion Coupled with Mass Spectrometry (GeLC-MS/MS)-Based Salivary Proteomic Profiling of Canine Oral Tumors. BMC Veterinary Research 2020, 16 (1), 335. https://doi.org/10.1186/s12917-020-02550-w.
Kottler, V. A.; Feron, R.; Nanda, I.; Klopp, C.; Du, K.; Kneitz, S.; Helmprobst, F.; Lamatsch, D. K.; Lopez-Roques, C.; Lluch, J.; Journot, L.; Parrinello, H.; Guiguen, Y.; Schartl, M. Independent Origin of XY and ZW Sex Determination Mechanisms in Mosquitofish Sister Species. Genetics 2020, 214 (1), 193–209. https://doi.org/10.1534/genetics.119.302698.
Salmona, J.; Olofsson, J. K.; Hong-Wa, C.; Razanatsoa, J.; Rakotonasolo, F.; Ralimanana, H.; Randriamboavonjy, T.; Suescun, U.; Vorontsova, M. S.; Besnard, G. Late Miocene Origin and Recent Population Collapse of the Malagasy Savanna Olive Tree (Noronhia Lowryi). Biological Journal of the Linnean Society 2020, 129 (1), 227–243. https://doi.org/10.1093/biolinnean/blz164.
Sommeria-Klein, G.; Zinger, L.; Coissac, E.; Iribar, A.; Schimann, H.; Taberlet, P.; Chave, J. Latent Dirichlet Allocation Reveals Spatial and Taxonomic Structure in a DNA-Based Census of Soil Biodiversity from a Tropical Forest. Molecular Ecology Resources 2020, 20 (2), 371–386. https://doi.org/10.1111/1755-0998.13109.
Dubois, C.; Martin, F.; Hassel, C.; Magnier, F.; Daumar, P.; Aubel, C.; Guerder, S.; Mounetou, E.; Penault-Lorca, F.; Bamdad, M. Low-Dose and Long-Term Olaparib Treatment Sensitizes MDA-MB-231 and SUM1315 Triple-Negative Breast Cancers Spheroids to Fractioned Radiotherapy. JCM 2019, 9 (1), 64. https://doi.org/10.3390/jcm9010064.
Leroy, T.; Rougemont, Q.; Dupouey, J.-L.; Bodénès, C.; Lalanne, C.; Belser, C.; Labadie, K.; Le Provost, G.; Aury, J.-M.; Kremer, A.; Plomion, C. Massive Postglacial Gene Flow between European White Oaks Uncovered Genes Underlying Species Barriers. New Phytol 2020, 226 (4), 1183–1197. https://doi.org/10.1111/nph.16039.
Orozco-Arias, S.; Piña, J. S.; Tabares-Soto, R.; Castillo-Ossa, L. F.; Guyot, R.; Isaza, G. Measuring Performance Metrics of Machine Learning Algorithms for Detecting and Classifying Transposable Elements. Processes 2020, 8 (6), 638. https://doi.org/10.3390/pr8060638.
Courtois, P.; Rorat, A.; Lemiere, S.; Guyoneaud, R.; Attard, E.; Longepierre, M.; Rigal, F.; Levard, C.; Chaurand, P.; Grosser, A.; Grobelak, A.; Kacprzak, M.; Lors, C.; Richaume, A.; Vandenbulcke, F. Medium-Term Effects of Ag Supplied Directly or via Sewage Sludge to an Agricultural Soil on Eisenia Fetida Earthworm and Soil Microbial Communities. Chemosphere 2020, 128761. https://doi.org/10.1016/j.chemosphere.2020.128761.
Aubé, J.; Senin, P.; Bonin, P.; Pringault, O.; Jeziorski, C.; Bouchez, O.; Klopp, C.; Guyoneaud, R.; Goñi-Urriza, M. Meta-Omics Provides Insights into the Impact of Hydrocarbon Contamination on Microbial Mat Functioning. Microbial Ecology 2020, 80 (2), 286–295. https://doi.org/10.1007/s00248-020-01493-x.
Bellec, L.; Cambon-Bonavita, M.-A.; Durand, L.; Aube, J.; Gayet, N.; Sandulli, R.; Brandily, C.; Zeppilli, D. Microbial Communities of the Shallow-Water Hydrothermal Vent Near Naples, Italy, and Chemosynthetic Symbionts Associated With a Free-Living Marine Nematode. Frontiers in Microbiology 2020, 11, 2023. https://doi.org/10.3389/fmicb.2020.02023.
Clerissi, C.; de Lorgeril, J.; Petton, B.; Lucasson, A.; Escoubas, J.-M.; Gueguen, Y.; Dégremont, L.; Mitta, G.; Toulza, E. Microbiota Composition and Evenness Predict Survival Rate of Oysters Confronted to Pacific Oyster Mortality Syndrome. Frontiers in Microbiology 2020, 11, 311. https://doi.org/10.3389/fmicb.2020.00311.
Milet, J.; Courtin, D.; Garcia, A.; Perdry, H. Mixed Logistic Regression in Genome-Wide Association Studies. BMC Bioinformatics 2020, 21 (1), 536. https://doi.org/10.1186/s12859-020-03862-2.
Marais, A.; Faure, C.; Lefebvre, M.; Lacombe, T.; Boursiquot, J.-M.; Candresse, T. Molecular Diversity of Grapevine Kizil Sapak Virus and Implications for Its Detection. Archives of Virology 2020, 165 (8), 1849–1853. https://doi.org/10.1007/s00705-020-04673-9.
Bazile, J.; Jaffrezic, F.; Dehais, P.; Reichstadt, M.; Klopp, C.; Laloe, D.; Bonnet, M. Molecular Signatures of Muscle Growth and Composition Deciphered by the Meta-Analysis of Age-Related Public Transcriptomics Data. Physiological Genomics 2020, 52 (8), 322–332. https://doi.org/10.1152/physiolgenomics.00020.2020.
García-Galán, A.; Nouvel, L.-X.; Baranowski, E.; Gómez-Martín, Á.; Sánchez, A.; Citti, C.; de la Fe, C. Mycoplasma Bovis in Spanish Cattle Herds: Two Groups of Multiresistant Isolates Predominate, with One Remaining Susceptible to Fluoroquinolones. Pathogens 2020, 9 (7), 545. https://doi.org/10.3390/pathogens9070545.
Racine, C.; Genêt, C.; Bourgneuf, C.; Dupont, C.; Plisson-Petit, F.; Sarry, J.; Hennequet-Antier, C.; Vigouroux, C.; Mathieu d’Argent, E.; Pierre, A.; Monniaux, D.; Fabre, S.; di Clemente, N. New Anti-Müllerian Hormone Target Genes Involved in Granulosa Cell Survival in Women with Polycystic Ovary Syndrome. The Journal of Clinical Endocrinology & Metabolism 2020, No. dgaa879. https://doi.org/10.1210/clinem/dgaa879.
Manzano-Marín, A. No Evidence for Wolbachia as a Nutritional Co-Obligate Endosymbiont in the Aphid Pentalonia Nigronervosa. Microbiome 2020, 8 (1), 72. https://doi.org/10.1186/s40168-020-00865-2.
Feutry, P.; Devloo‐Delva, F.; Tran Lu Y, A.; Mona, S.; Gunasekera, R. M.; Johnson, G.; Pillans, R. D.; Jaccoud, D.; Kilian, A.; Morgan, D. L.; Saunders, T.; Bax, N. J.; Kyne, P. M. One Panel to Rule Them All: DArTcap Genotyping for Population Structure, Historical Demography, and Kinship Analyses, and Its Application to a Threatened Shark. Mol Ecol Resour 2020, 20 (6), 1470–1485. https://doi.org/10.1111/1755-0998.13204.
Borvető, F.; Bravo, I. G.; Willemsen, A. Papillomaviruses Infecting Cetaceans Exhibit Signs of Genome Adaptation Following a Recombination Event. Virus Evolution 2020, 6 (1), veaa038. https://doi.org/10.1093/ve/veaa038.
Pedro, N.; Brucato, N.; Fernandes, V.; André, M.; Saag, L.; Pomat, W.; Besse, C.; Boland, A.; Deleuze, J.-F.; Clarkson, C.; Sudoyo, H.; Metspalu, M.; Stoneking, M.; Cox, M. P.; Leavesley, M.; Pereira, L.; Ricaut, F.-X. Papuan Mitochondrial Genomes and the Settlement of Sahul. Journal of Human Genetics 2020, 65 (10), 875–887. https://doi.org/10.1038/s10038-020-0781-3.
Noyer, M.; Reoyo-Prats, B.; Aubert, D.; Bernard, M.; Verneau, O.; Palacios, C. Particle-Attached Riverine Bacteriome Shifts in a Pollutant-Resistant and Pathogenic Community during a Mediterranean Extreme Storm Event. Science of The Total Environment 2020, 732, 139047. https://doi.org/10.1016/j.scitotenv.2020.139047.
Roujol, D.; Hoffmann, L.; Clemente, H. S.; Schmitt-Keichinger, C.; Ritzenthaler, C.; Burlat, V.; Jamet, E. Plant Cell Wall Proteomes: Bioinformatics and Cell Biology Tools to Assess the Bona Fide Cell Wall Localization of Proteins. In The Plant Cell Wall; Popper, Z. A., Ed.; Springer New York: New York, NY, 2020; Vol. 2149, pp 443–462. https://doi.org/10.1007/978-1-0716-0621-6_25.
Demenou, B. B.; Migliore, J.; Heuertz, M.; Monthe, F. K.; Ojeda, D. I.; Wieringa, J. J.; Dauby, G.; Albreht, L.; Boom, A.; Hardy, O. J. Plastome Phylogeography in Two African Rain Forest Legume Trees Reveals That Dahomey Gap Populations Originate from the Cameroon Volcanic Line. Molecular Phylogenetics and Evolution 2020, 150, 106854. https://doi.org/10.1016/j.ympev.2020.106854.
Roques, S.; Deborde, C.; Richard, N.; Marchand, Y.; Larroquet, L.; Prigent, S.; Skiba-Cassy, S.; Moing, A.; Fauconneau, B. Proton-NMR Metabolomics of Rainbow Trout Fed a Plant-Based Diet Supplemented with Graded Levels of a Protein-Rich Yeast Fraction Reveal Several Metabolic Processes Involved in Growth. The Journal of Nutrition 2020, 150 (9), 2268–2277. https://doi.org/10.1093/jn/nxaa206.
Brouard, C.; de Givry, S.; Schiex, T. Pushing Data into CP Models Using Graphical Model Learning and Solving. In Principles and Practice of Constraint Programming; Simonis, H., Ed.; Lecture Notes in Computer Science; Springer International Publishing: Cham, 2020; Vol. 12333, pp 811–827. https://doi.org/10.1007/978-3-030-58475-7_47.
Genevière, A.-M.; Derelle, E.; Escande, M.-L.; Grimsley, N.; Klopp, C.; Ménager, C.; Michel, A.; Moreau, H. Responses to Iron Oxide and Zinc Oxide Nanoparticles in Echinoderm Embryos and Microalgae: Uptake, Growth, Morphology, and Transcriptomic Analysis. Nanotoxicology 2020, 1–20. https://doi.org/10.1080/17435390.2020.1827074.
Toyama, K. S.; Crochet, P.-A.; Leblois, R. Sampling Schemes and Drift Can Bias Admixture Proportions Inferred by Structure. Molecular Ecology Resources 2020, 20 (6), 1769–1785. https://doi.org/10.1111/1755-0998.13234.
Huot, C.; Clerissi, C.; Gourbal, B.; Galinier, R.; Duval, D.; Toulza, E. Schistosomiasis Vector Snails and Their Microbiota Display a Phylosymbiosis Pattern. Front. Microbiol. 2020, 10, 3092. https://doi.org/10.3389/fmicb.2019.03092.
Liu, Y.; Blain, S.; Crispi, O.; Rembauville, M.; Obernosterer, I. Seasonal Dynamics of Prokaryotes and Their Associations with Diatoms in the Southern Ocean as Revealed by an Autonomous Sampler. Environ Microbiol 2020, 22 (9), 3968–3984. https://doi.org/10.1111/1462-2920.15184.
Manzano-Marı́n, A.; Coeur d’acier, A.; Clamens, A.-L.; Orvain, C.; Cruaud, C.; Barbe, V.; Jousselin, E. Serial Horizontal Transfer of Vitamin-Biosynthetic Genes Enables the Establishment of New Nutritional Symbionts in Aphids’ Di-Symbiotic Systems. The ISME Journal 2020, 14 (1), 259–273. https://doi.org/10.1038/s41396-019-0533-6.
Wen, M.; Feron, R.; Pan, Q.; Guguin, J.; Jouanno, E.; Herpin, A.; Klopp, C.; Cabau, C.; Zahm, M.; Parrinello, H.; Journot, L.; Burgess, S. M.; Omori, Y.; Postlethwait, J. H.; Schartl, M.; Guiguen, Y. Sex Chromosome and Sex Locus Characterization in Goldfish, Carassius Auratus (Linnaeus, 1758). BMC Genomics 2020, 21 (1), 552. https://doi.org/10.1186/s12864-020-06959-3.
Klopp, C.; Cabau, C.; Greif, G.; Lasalle, A.; Di Landro, S.; Vizziano-Cantonnet, D. Siberian Sturgeon Multi-Tissue Reference Transcriptome Database. Database 2020, 2020 (baaa082). https://doi.org/10.1093/database/baaa082.
Pont, F.; Tosolini, M.; Gao, Q.; Perrier, M.; Madrid-Mencía, M.; Huang, T. S.; Neuvial, P.; Ayyoub, M.; Nazor, K.; Fournié, J.-J. Single-Cell Virtual Cytometer Allows User-Friendly and Versatile Analysis and Visualization of Multimodal Single Cell RNAseq Datasets. NAR Genomics and Bioinformatics 2020, 2 (lqaa025). https://doi.org/10.1093/nargab/lqaa025.
Lallias, D.; Bernard, M.; Ciobotaru, C.; Dechamp, N.; Labbé, L.; Goardon, L.; Le Calvez, J.-M.; Bideau, M.; Fricot, A.; Prézelin, A.; Charles, M.; Moroldo, M.; Cousin, X.; Bouchez, O.; Roulet, A.; Quillet, E.; Dupont-Nivet, M. Sources of Variation of DNA Methylation in Rainbow Trout: Combined Effects of Temperature and Genetic Background. null 2020, 1–22. https://doi.org/10.1080/15592294.2020.1834924.
Villette, P.; Afonso, E.; Couval, G.; Levret, A.; Galan, M.; Goydadin, A.-C.; Cosson, J.-F.; Giraudoux, P. Spatio-Temporal Trends in Richness and Persistence of Bacterial Communities in Decline-Phase Water Vole Populations. Sci Rep 2020, 10 (1), 9506. https://doi.org/10.1038/s41598-020-66107-5.
Broseus, L.; Thomas, A.; Oldfield, A. J.; Severac, D.; Dubois, E.; Ritchie, W. TALC: Transcript-Level Aware Long-Read Correction. Bioinformatics 2020, No. btaa634. https://doi.org/10.1093/bioinformatics/btaa634.
Frank, X.; Radjaï, F.; Nezamabadi, S.; Delenne, J.-Y. Tensile Strength of Granular Aggregates: Stress Chains across Particle Phase versus Stress Concentration by Pores. Phys. Rev. E 2020, 102 (2), 022906. https://doi.org/10.1103/PhysRevE.102.022906.
Jouneau, L.; Lefebvre, D. J.; Costa, F.; Romey, A.; Blaise-Boisseau, S.; Relmy, A.; Jaszczyszyn, Y.; Dard-Dascot, C.; Déjean, S.; Versillé, N.; Guitton, E.; Hudelet, P.; Curet, M.; De Clercq, K.; Bakkali-Kassimi, L.; Zientara, S.; Klonjkowski, B.; Schwartz-Cornil, I. The Antibody Response Induced FMDV Vaccines in Sheep Correlates with Early Transcriptomic Responses in Blood. npj Vaccines 2020, 5 (1), 1. https://doi.org/10.1038/s41541-019-0151-3.
Yacoub, A.; Magnin, N.; Gerbore, J.; Haidar, R.; Bruez, E.; Compant, S.; Guyoneaud, R.; Rey, P. The Biocontrol Root-Oomycete, Pythium Oligandrum, Triggers Grapevine Resistance and Shifts in the Transcriptome of the Trunk Pathogenic Fungus, Phaeomoniella Chlamydospora. IJMS 2020, 21 (18), 6876. https://doi.org/10.3390/ijms21186876.
Rouïl, J.; Jousselin, E.; Coeur d’acier, A.; Cruaud, C.; Manzano-Marín, A. The Protector within: Comparative Genomics of APSE Phages across Aphids Reveals Rampant Recombination and Diverse Toxin Arsenals. Genome Biology and Evolution 2020, 12 (6), 878–889. https://doi.org/10.1093/gbe/evaa089.
Du, K.; Stöck, M.; Kneitz, S.; Klopp, C.; Woltering, J. M.; Adolfi, M. C.; Feron, R.; Prokopov, D.; Makunin, A.; Kichigin, I.; Schmidt, C.; Fischer, P.; Kuhl, H.; Wuertz, S.; Gessner, J.; Kloas, W.; Cabau, C.; Iampietro, C.; Parrinello, H.; Tomlinson, C.; Journot, L.; Postlethwait, J. H.; Braasch, I.; Trifonov, V.; Warren, W. C.; Meyer, A.; Guiguen, Y.; Schartl, M. The Sterlet Sturgeon Genome Sequence and the Mechanisms of Segmental Rediploidization. Nature Ecology & Evolution 2020, 4 (6), 841–852. https://doi.org/10.1038/s41559-020-1166-x.
Dimeglio, C.; Raymond, S.; Jeanne, N.; Reynes, C.; Carcenac, R.; Lefebvre, C.; Cazabat, M.; Nicot, F.; Delobel, P.; Izopet, J. THETA: A New Genotypic Approach for Predicting HIV-1 CRF02-AG Coreceptor Usage. Bioinformatics 2020, 36 (2), 416–421. https://doi.org/10.1093/bioinformatics/btz585.
Orozco-Arias, S.; Tobon-Orozco, N.; Piña, J. S.; Jiménez-Varón, C. F.; Tabares-Soto, R.; Guyot, R. TIP_finder: An HPC Software to Detect Transposable Element Insertion Polymorphisms in Large Genomic Datasets. Biology 2020, 9 (9), 281. https://doi.org/10.3390/biology9090281.
Mahiddine, K.; Hassel, C.; Murat, C.; Girard, M.; Guerder, S. Tissue-Specific Factors Differentially Regulate the Expression of Antigen-Processing Enzymes During Dendritic Cell Ontogeny. Frontiers in Immunology 2020, 11, 453. https://doi.org/10.3389/fimmu.2020.00453.
Perrier, F.; Bertucci, A.; Pierron, F.; Feurtet‐Mazel, A.; Simon, O.; Klopp, C.; Candaudap, F.; Pokrovski, O.; Etcheverria, B.; Mornet, S.; Baudrimont, M. Transfer and Transcriptomic Profiling in Liver and Brain of European Eels ( Anguilla Anguilla ) After Diet‐borne Exposure to Gold Nanoparticles. Environ Toxicol Chem 2020, 39 (12), 2450–2461. https://doi.org/10.1002/etc.4858.
Capt, C.; Bouvet, K.; Guerra, D.; Robicheau, B. M.; Stewart, D. T.; Pante, E.; Breton, S. Unorthodox Features in Two Venerid Bivalves with Doubly Uniparental Inheritance of Mitochondria. Sci Rep 2020, 10 (1), 1087. https://doi.org/10.1038/s41598-020-57975-y.
Clerissi, C.; Guillou, L.; Escoubas, J.-M.; Toulza, E. Unveiling Protist Diversity Associated with the Pacific Oyster Crassostrea Gigas Using Blocking and Excluding Primers. BMC Microbiology 2020, 20 (1), 193. https://doi.org/10.1186/s12866-020-01860-1.
Khimoun, A.; Doums, C.; Molet, M.; Kaufmann, B.; Peronnet, R.; Eyer, P. A.; Mona, S. Urbanization without Isolation: The Absence of Genetic Structure among Cities and Forests in the Tiny Acorn Ant Temnothorax Nylanderi. Biol Lett 2020, 16 (1), 20190741. https://doi.org/10.1098/rsbl.2019.0741.
Talouarn, E.; Teissier, M.; Bardou, P.; Larroque, H.; Clément, V.; Palhière, I.; Tosser-Klopp, G.; Rupp, R.; Robert-Granié, C. Using Sequence Variants of a QTL Region Improves the Accuracy of Genomic Evaluation in French Saanen Goats. Journal of Dairy Science 2020. https://doi.org/10.3168/jds.2020-18837.
Muranty, H.; Denancé, C.; Feugey, L.; Crépin, J.-L.; Barbier, Y.; Tartarini, S.; Ordidge, M.; Troggio, M.; Lateur, M.; Nybom, H.; Paprstein, F.; Laurens, F.; Durel, C.-E. Using Whole-Genome SNP Data to Reconstruct a Large Multi-Generation Pedigree in Apple Germplasm. BMC Plant Biol 2020, 20 (1), 2. https://doi.org/10.1186/s12870-019-2171-6.
Ouali, A.; Allouche, D.; de Givry, S.; Loudni, S.; Lebbah, Y.; Loukil, L.; Boizumault, P. Variable Neighborhood Search for Graphical Model Energy Minimization. Artificial Intelligence 2020, 278, 103194. https://doi.org/10.1016/j.artint.2019.103194.
Touchard, A.; Aili, S. R.; Téné, N.; Barassé, V.; Klopp, C.; Dejean, A.; Kini, R. M.; Mrinalini; Coquet, L.; Jouenne, T.; Lefranc, B.; Leprince, J.; Escoubas, P.; Nicholson, G. M.; Treilhou, M.; Bonnafé, E. Venom Peptide Repertoire of the European Myrmicine Ant Manica Rubida : Identification of Insecticidal Toxins. J. Proteome Res. 2020, 19 (4), 1800–1811. https://doi.org/10.1021/acs.jproteome.0c00048.
Yau, S.; Krasovec, M.; Benites, L. F.; Rombauts, S.; Groussin, M.; Vancaester, E.; Aury, J.-M.; Derelle, E.; Desdevises, Y.; Escande, M.-L.; Grimsley, N.; Guy, J.; Moreau, H.; Sanchez-Brosseau, S.; van de Peer, Y.; Vandepoele, K.; Gourbiere, S.; Piganeau, G. Virus-Host Coexistence in Phytoplankton through the Genomic Lens. Sci. Adv. 2020, 6 (14), eaay2587. https://doi.org/10.1126/sciadv.aay2587.