Publications

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

2025

1. Almeida, M.M., Cabrita, E., Laizé, V., Brionne, A., Labbé, C., and Fatsini, E. (2025). Cryopreservation did not affect spermatogonia global methylation profile in Senegalese sole (Solea senegalensis). Cryobiology 118, 105162. https://doi.org/10.1016/j.cryobiol.2024.105162.

2. Alonso-García, M., Liaubet, L., Faraut, T., Dehais, P., Kühn, C., Demars, J., Gutiérrez-Gil, B., and Robic, A. (2025). Decoupling transcriptome layers: The distinct and variable nature of circular RNAs. BMC Biology 23, 269. https://doi.org/10.1186/s12915-025-02375-9.

3. Antonios, S., Rodríguez-Ramilo, S.T., Legarra, A., Astruc, J.-M., Varona, L., and Vitezica, Z.G. (2025). Genetic inbreeding load and its individual prediction for milk yield in French dairy sheep. Genetics Selection Evolution 57, 1. https://doi.org/10.1186/s12711-024-00945-z.

4. Araújo, N.H., Landry, D., Quilbé, J., Pervent, M., Nouwen, N., Klopp, C., Cullimore, J., Gully, D., Vicedo, C., Gasciolli, V., Brottier, L., Pichereaux, C., Racoupeau, M., Rios, M., Gressent, F., Chaintreuil, C., Gough, C., Giraud, E., Lefebvre, B., and Arrighi, J.-F. (2025). The receptor-like cytoplasmic kinase AeRLCK2 mediates Nod-independent rhizobial symbiosis in aeschynomene legumes. The Plant Cell 37, koaf201. https://doi.org/10.1093/plcell/koaf201.

5. Barberoux, V., Anzil, A., Meinertzhagen, L., Nguyen-Dinh, T., Servais, P., and George, I.F. (2025). Spatio–temporal dynamics of bacterial community composition in a Western European watershed, the Meuse River watershed. FEMS Microbiology Ecology 101, fiaf022. https://doi.org/10.1093/femsec/fiaf022.

6. Barka, I., Dujardin, E., Dewaele, A., André, M., Frambourg, A., Thépot, D., Jouneau, L., Le Danvic, C., Jolivet, G., Pannetier, M., Mandon-Pépin, B., and Pailhoux, E. (2025). DMRT1 haploinsufficiency leads to secondary infertility in XY male rabbits. Biology of Reproduction 113, 450–465. https://doi.org/10.1093/biolre/ioaf064.

7. Beaumont, C., Prigent, S., Mori, K., Baldet, P., Jorly, J., Randriafanomezantsoa-Radohery, G., Beauvoit, B., Pateyron, S., Delannoy, E., Pétriacq, P., Gibon, Y., and Colombié, S. (2025). Interspecies predictions of growth traits from quantitative transcriptome data acquired during fruit development. Journal of Experimental Botany 76, 3390–3411. https://doi.org/10.1093/jxb/eraf122.

8. Belinchon-Moreno, J., Berard, A., Canaguier, A., Le-Clainche, I., Rittener-Ruff, V., Lagnel, J., Hinsinger, D., Boissot, N., and Faivre-Rampant, P. (2025). Nuclear and organelle genome assemblies of 5 Cucumis melo L. Accessions, Ananas, Canton, PI 414723, Vedrantais, and Zhimali, belonging to diverse botanical groups. G3: Genes, Genomes, Genetics 15, jkaf098. https://doi.org/10.1093/g3journal/jkaf098.

9. Belloy, M., Schmitt, B.A.M., Marty, F.H., Paut, C., Bassot, E., Aïda, A., Alis, M., Zahm, M., Chaubet, A., Garnier, H., Flores-Aguilar, T., Roitg, E., Gutierrez-Loli, R., Allart, S., Ecalard, R., Boursereau, R., Ligat, G., Gonzalez-Dunia, D., Blanchard, N., and Suberbielle, E. (2025). Toxoplasma gondii infection and chronic IL-1 elevation drive hippocampal DNA double-strand break signaling, leading to cognitive deficits. Nature Neuroscience 28, 2067–2077. https://doi.org/10.1038/s41593-025-02041-x.

10. Berard, A., Pradel, J., Charbonnel, N., and Galan, M. (2025). Spider Webs, Soil or Leaf Swabs to Detect Environmental DNA From Terrestrial Vertebrates: What Is the Best Substrate? Molecular Ecology Resources 25, e70037. https://doi.org/10.1111/1755-0998.70037.

11. Berger, M.M.J., Garcia, V., Lacrampe, N., Rubio, B., Decros, G., Pétriacq, P., Flandin, A., Cassan, C., Hilbert-Masson, G., Colombié, S., Atanassova, R., and Gallusci, P. (2025). Grapevine cell response to carbon deficiency requires transcriptome and methylome reprogramming. Horticulture Research 12, uhae277. https://doi.org/10.1093/hr/uhae277.

12. Bessière, C., Meggetto, F., Gaspin, C., and Fuchs, S. (2025). Identification of Circular RNA Variants by Oxford Nanopore Long-Read Sequencing. In Gene Expression Analysis, N. Raghavachari and N. Garcia-Reyero, eds. (Springer US), pp. 49–68. https://doi.org/10.1007/978-1-0716-4276-4_3.

13. Bochereau, P., Maman Haddad, S., Le Bihan-Duval, E., and Berri, C. (2025). RNA-Seq data provide new insights into the molecular regulation of breast muscle glycogen reserves, a key factor in muscle function and meat quality in chickens. Poultry Science 104, 105136. https://doi.org/10.1016/j.psj.2025.105136.

14. Bonnier, J., Sáez Laguna, E., Francisco, T., Troispoux, V., Brunaux, O., Schmitt, S., Traissac, S., Tysklind, N., and Heuertz, M. (2025). Wet Season Environments Drive Local Adaptation in the Timber Tree Dicorynia guianensis in French Guiana. Molecular Ecology 34, e17759. https://doi.org/10.1111/mec.17759.

15. Boussaha, M., Eché, C., Klopp, C., Grohs, C., Milhes, M., Suin, A., Bulach, T., Fourdin, R., Faraut, T., Kuchly, C., Fritz, S., Vernette, C., Naji, M., Sorin, V., Capitan, A., Gaspin, C., Milan, D., Boichard, D., Iampietro, C., and Donnadieu, C. (2025). Whole genome short read data from 567 bulls of 14 breeds provides insight into genetic diversity of French cattle. Data in Brief 62, 112049. https://doi.org/10.1016/j.dib.2025.112049.

16. Bravo De Laguna, F., Achard, C.S., Dunière, L., Parmentier, E., Helmja, K., Bertaud, B., Lebreton, P., Saornil, D., Chevaux, E., Castex, M., and Apper, E. (2025). In vitro characterization of amino acid digestibility and fermentative properties of a specific hydrolyzed yeast, and its in vivo effects on growth performance and fecal microbiota in weanling piglets. Frontiers in Nutrition 12, 1596561. https://doi.org/10.3389/fnut.2025.1596561.

17. Briand, M., Jacques, M.-A., and Dittmer, J. (2025). The hidden life of xylella : Mining the NCBI Sequence Read Archive reveals potential new species, host plants, and infected areas for this elusive bacterial plant pathogen. Applied and Environmental Microbiology 91, e00913–25. https://doi.org/10.1128/aem.00913-25.

18. Brucato, N., Lisant, V., Kinipi, C., Kik, A., Besnard, G., Leavesley, M., and Ricaut, F.-X. (2025). Influence of betel nut chewing on oral microbiome in Papua New Guinea. Evolution, Medicine, and Public Health 13, 36–44. https://doi.org/10.1093/emph/eoae030.

19. Burnard, C., Mancheron, A., and Ritchie, W. (2025). Generating realistic artificial human genomes using adversarial autoencoders. NAR Genomics and Bioinformatics 7, lqaf101. https://doi.org/10.1093/nargab/lqaf101.

20. Caillaud, M.-A., Audonnet, M., Couderc, C., Thierry, A., Maillard, M.-B., Doutart, E., Laroute, V., Cocaign-Bousquet, M., Tormo, H., and Daveran-Mingot, M.-L. (2025). Interaction between a Lactococcus lactis autochthonous starter and a raw goat milk microbial community during long-term backslopping. Food Microbiology 125, 104656. https://doi.org/10.1016/j.fm.2024.104656.

21. Camus, L., Rode, N.O., Serga, S., Loiseau, A., Chen, X., Iampietro, C., Kenis, M., Marande, W., Mensch, J., Parinello, H., Savić Veselinović, M., Valière, S., Zhang, J., Estoup, A., Boitard, S., and Gautier, M. (2025). Adaptive Challenges of Past and Future Invasion of Drosophila suzukii : Insights From Novel Genomic Resources and Statistical Methods Combining Individual and Pool Sequencing Data. Molecular Ecology 34, e70192. https://doi.org/10.1111/mec.70192.

22. Chalabi, S., Loonen, L., Boekhorst, J., Li, H., Fang, L., Harrison, P.W., Lakhal, W., Lluch, J., Sokolov, A., Djebali, S., Rau, A., Giuffra, E., and Wells, J. (2025). Differences in maternal diet fiber content influence patterns of gene expression and chromatin accessibility in fetuses and piglets. Genomics 117, 110995. https://doi.org/10.1016/j.ygeno.2025.110995.

23. Changey, F., Merlin, C., Fourrier, C., Fontaine, P., and Mathieu, L. (2025). Identifying the Effects of Fish and Rhizosphere on the Structure of the Planktonic Bacterial Communities and Resistome in an Aquaponics Recirculation Loop. Environmental Microbiology Reports 17, e70128. https://doi.org/10.1111/1758-2229.70128.

24. Charbonnel, E., Benoit, L., Nidelet, S., Ortega‐Abboud, E., Gschloessl, B., Leblois, R., Ouvrard, D., and Chapuis, M. (2025). Optimization and Evaluation of the bestRAD Sequencing Approach: Towards Ascertainment of the Invasion Routes of the Oriental Fruit Fly, Bactrocera dorsalis. Molecular Ecology Resources 25, e14114. https://doi.org/10.1111/1755-0998.14114.

25. Colinet, D., Haon, M., Drula, E., Boyer, M., Grisel, S., Belliardo, C., Koutsovoulos, G.D., Berrin, J.-G., and Danchin, E.G.J. (2025). Functional Carbohydrate-Active Enzymes Acquired by Horizontal Gene Transfer from Plants in the Whitefly Bemisia tabaci. Genome Biology and Evolution 17, evaf012. https://doi.org/10.1093/gbe/evaf012.

26. Combes, S., Knudsen, C., Rumeau, M., Pascal, G., Cauquil, L., Helies, V., Ruesche, J., Poli, M., Jones, E., Lencina, C., Castinel, A., Averty, E., Venot, E., Cholet, S., Beaumont, M., and Fenaille, F. (2025). The Diversity of Oligosaccharide Composition in Rabbit Milk and Its Association with the Development of the Cecal Microbiota and the Survival of Young Rabbits. The Journal of Nutrition 155, 4222–4238. https://doi.org/10.1016/j.tjnut.2025.10.013.

27. Cooke, J., Wieder, C., Poupin, N., Frainay, C., Ebbels, T., and Jourdan, F. (2025). Simulated metabolic profiles reveal biases in pathway analysis methods. Metabolomics 21, 136. https://doi.org/10.1007/s11306-025-02335-y.

28. Cousson, A., Mahé, F., Guyet, U., Razafimahafaly, D., and Bernard, L. (2025). NanoASV: A snakemake workflow for reproducible field-based Nanopore full-length 16S metabarcoding amplicon data analysis. Bioinformatics 41, btaf089. https://doi.org/10.1093/bioinformatics/btaf089.

29. Cousson, A., Pablo, A.-L., Cournac, L., Piton, G., Dezette, D., Robin, A., Taschen, E., and Bernard, L. (2025). Ultra pure high molecular weight DNA from soil for Nanopore shotgun metagenomics and metabarcoding sequencing. MethodsX 14, 103134. https://doi.org/10.1016/j.mex.2024.103134.

30. Darriaut, R., Lailheugue, V., Wastin, J., Tran, J., Martins, G., Ballestra, P., Masneuf-Pomarède, I., Ollat, N., and Lauvergeat, V. (2025). Rhizobacteria from vineyard and commercial arbuscular mycorrhizal fungi induce synergistic microbiome shifts within grapevine root systems. Scientific Reports 15, 27884. https://doi.org/10.1038/s41598-025-12673-5.

31. Delesalle, C., Montiel-Jorda, A., Aiba, R., Spielmann, J., Neveu, J., Fujita, S., and Vert, G. (2025). Arabidopsis Microtubule-BRI1 Associated Proteins negatively regulate hypocotyl elongation by controlling brassinosteroid-dependent cortical microtubule reorientation. Plant Communications, 101637. https://doi.org/10.1016/j.xplc.2025.101637.

32. Delrieu-Trottin, E., Ben Chéhida, S., Sukmono, T., Dahruddin, H., Sholihah, A., Kustiati, K., Fitriana, Y., Muchlisin, Z.A., Elvyra, R., Wibowo, A., Utama, I.V., Nurhaman, U., Sauri, S., Risdawati, R., Zein, M.S.A., Pouzadoux, J., Agnèse, J.-F., Tilak, M.-K., Page, L.M., Von Rintelen, T., Wowor, D., Steinke, D., Mona, S., Rüber, L., Hebert, P.D.N., and Hubert, N. (2025). Aquatic Biotas of Sundaland Are Fragmented But Not Refugial. Systematic Biology 74, 685–699. https://doi.org/10.1093/sysbio/syaf005.

33. Derriche, M., Nouvel, L.X., Gaudino, M., Sagné, E., Simon, E., Robert, H., Pot, G., Meyer, G., De La Fe, C., Arfi, Y., Maillard, R., Citti, C., and Baranowski, E. (2025). Bacterial conjugation in the ruminant pathogen Mycoplasma agalactiae is influenced by eukaryotic host factors. Applied and Environmental Microbiology 91, e00868–25. https://doi.org/10.1128/aem.00868-25.

34. Diot, A., Madignier, G., Di Valentin, O., Djari, A., Maza, E., Chen, Y., Blanchet, S., and Chervin, C. (2025). Responses of grapevine cells to physiological doses of ethanol, including induced resistance to heat stress. Plant Biology 27, 1187–1201. https://doi.org/10.1111/plb.70064.

35. Dufour, A., Rossignol, M.-N., Manceau, P., Bailly, Y., Ferchaud, S., Mercat, M.-J., Turhan, A.G., Djebali, S., Foissac, S., Artus, J., and Acloque, H. (2025). Single-cell omics uncover gene dynamics shaping embryonic and extra embryonic lineages in pig blastocysts. iScience, 114519. https://doi.org/10.1016/j.isci.2025.114519.

36. Durand, K., Ogier, J.-C., and Nam, K. (2025). The evaluation of shotgun sequencing and rpoB metabarcoding for taxonomic profiling of bacterial communities. BMC Microbiology 25, 413. https://doi.org/10.1186/s12866-025-04149-3.

37. Duval, H., Heurtevin, L., Dlalah, N., Caravel, C., Callot, C., and Van Ghelder, C. (2025). Identification and expression of the peach TNL RMia genes for the resistance to the root-knot nematode Meloidogyne incognita. Scientia Horticulturae 343, 114081. https://doi.org/10.1016/j.scienta.2025.114081.

38. Dvorak, E., Mazet, I.D., Couture, C., Delmotte, F., and Foulongne-Oriol, M. (2025). Recombination landscape and karyotypic variations revealed by linkage mapping in the grapevine downy mildew pathogen Plasmopara viticola. G3: Genes, Genomes, Genetics 15, jkae259. https://doi.org/10.1093/g3journal/jkae259.

39. Etourneau, A., Rupp, R., and Servin, B. (2025). Genome landscape and genetic architecture of recombination in domestic goats (Capra hircus). Genetics Selection Evolution 57, 57. https://doi.org/10.1186/s12711-025-01001-0.

40. Eynard, S.E., Mondet, F., Basso, B., Bouchez, O., Le Conte, Y., Dainat, B., Decourtye, A., Genestout, L., Guichard, M., Guillaume, F., Labarthe, E., Locke, B., Mahla, R., De Miranda, J., Neuditschko, M., Phocas, F., Canale‐Tabet, K., Vignal, A., and Servin, B. (2025). Sequence‐Based Multi Ancestry Association Study Reveals the Polygenic Architecture of Varroa destructor Resistance in the Honeybee Apis mellifera. Molecular Ecology 34, e17637. https://doi.org/10.1111/mec.17637.

41. Gautier, A., Laval, V., and Balesdent, M.-H. (2025). MPSeqM, a tool combining multiplex PCR and high-throughput sequencing to study the polymorphism of eight Leptosphaeria maculans avirulence genes and its application to field surveys in France. BMC Microbiology 25, 159. https://doi.org/10.1186/s12866-025-03855-2.

42. Gricourt, G., and Faulon, J.-L. (2025). BioRGroup dataset: R-group expansion of ChEBI molecules referenced in the Rhea database. Scientific Data 12, 1692. https://doi.org/10.1038/s41597-025-05983-w.

43. Harlé, O., Parayre, S., Maillard, M., Henry, G., Guédon, É., Thierry, A., Niay, J., Deutsch, S., and Falentin, H. (2025). Fermentation of Soy Juice by Lactiplantibacillus plantarum CIRM‐BIA777 Produces Flavor‐Related and Health‐Promoting Metabolites. Food Frontiers 6, 3137–3153. https://doi.org/10.1002/fft2.70118.

44. Hesson, J.C., Haba, Y., McBride, C.S., Sheerin, E., Mathers, T.C., Paulini, M., Pointon, D.-L.B., Torrance, J.W., Sadasivan Baby, C., Wood, J.M.D., Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, McCarthy, S.A., Lawniczak, M.K.N., and Makunin, A. (2025). A chromosomal reference genome sequence for the northern house mosquito, Culex pipiens form pipiens, Linnaeus, 1758. Wellcome Open Research 10, 107. https://doi.org/10.12688/wellcomeopenres.23767.1.

45. Huertas, C., Coulibaly, A.B., Payros, D., Penary, M., Puel, S., Naylies, C., Payros, G., Lippi, Y., Oswald, I.P., Mirey, G., and Vignard, J. (2025). Genotoxic interaction between deoxynivalenol and acrylamide. Food Research International 214, 116633. https://doi.org/10.1016/j.foodres.2025.116633.

46. Iannuccelli, N., Valière, S., Sarry, J., Donnadieu, C., and Demars, J. (2025). An optimized protocol to detect high‐throughput DNA methylation from custom targeted sequences on 96 samples simultaneously. FEBS Open Bio 15, 1918–1929. https://doi.org/10.1002/2211-5463.70093.

47. Jorge, E., Foissac, S., Neuvial, P., Zytnicki, M., and Vialaneix, N. (2025). A comprehensive review and benchmark of differential analysis tools for Hi-C data. Briefings in Bioinformatics 26, bbaf074. https://doi.org/10.1093/bib/bbaf074.

48. Kalachova, T., Jindřichová, B., Blouin, M., Pospíchalová, R., Burketová, L., Ruelland, E., and Puga-Freitas, R. (2025). Artificial selection of suppressive or conducive rhizosphere microbiota circumvents the growth–defense trade-off due to a foliar pathogen. Plant Stress, 101215. https://doi.org/10.1016/j.stress.2025.101215.

49. Karami, K., Sabban, J., Cerutti, C., Devailly, G., Foissac, S., Gourichon, D., Hubert, A., Hubert, J.-N., Leroux, S., Zerjal, T., Lagarrigue, S., and Pitel, F. (2025). Molecular responses of chicken embryos to maternal heat stress through DNA methylation and gene expression: A pilot study. Environmental Epigenetics 11, dvaf009. https://doi.org/10.1093/eep/dvaf009.

50. Keller, J., Plaisancié, P., Fouché, E., Pralet, E.-M., Naud, N., Blas-Y-Estrada, F., Maslo, C., Ahn, I., Chevolleau, S., Meireles, M.-H., Héliès-Toussaint, C., Pietri, S., Cassien, M., Khoury, L., Audebert, M., Pierre, F., Theodorou, V., Olier, M., and Guéraud, F. (2025). Heme iron amplifies azoxymethane initiating effect on rat colon preneoplastic lesions. Redox Experimental Medicine 2025, e250001. https://doi.org/10.1530/REM-25-0001.

51. Koffi, A.D., Babin, R., Delvare, G., Chérasse, S., Ouvrard, D., Shimbori, E., Koigny, K.J., Kpangui, S., Benoit, L., Galan, M., Yodé, C., Ouali N’goran, M., and Haran, J. (2025). A barcode database for insects associated with the spread of the Cocoa Swollen Shoot Virus Disease in Côte d’Ivoire. Biodiversity Data Journal 13, e144017. https://doi.org/10.3897/BDJ.13.e144017.

52. Labory, J., Boulaimen, Y., Singh, J., Ait-El-Mkadem Saadi, S., Paquis-Flucklinger, V., Bannwarth, S., and Bottini, S. (2025). Accelerate the discovery of genetic variants in mitochondrial diseases with Variant prIOritization using Latent spAce. Briefings in Bioinformatics 26, bbaf612. https://doi.org/10.1093/bib/bbaf612.

53. Lapalu, N., Lamothe, L., Petit, Y., Genissel, A., Delude, C., Feurtey, A., Abraham, L.N., Smith, D., King, R., Renwick, A., Appertet, M., Sucher, J., Steindorff, A.S., Goodwin, S.B., Kema, G.H.J., Grigoriev, I.V., Hane, J., Rudd, J., Stukenbrock, E., Croll, D., Scalliet, G., and Lebrun, M.-H. (2025). Improved Gene Annotation of the Fungal Wheat Pathogen Zymoseptoria tritici Based on Combined Iso-Seq and RNA-Seq Evidence. Molecular Plant-Microbe Interactions®, MPMI-07-25-0077-TA. https://doi.org/10.1094/MPMI-07-25-0077-TA.

54. Laroche, N., Grimm, P., Julliand, S., and Sorci, G. (2025). Combining in vivo and in vitro approaches to investigate the effect of sainfoin on strongyle infection, immunity, and large intestine ecosystem of horses. Journal of Animal Science 103, skaf100. https://doi.org/10.1093/jas/skaf100.

55. Laso-Jadart, R., Corrigan, S.L., Yang, L., Lee, S.-H., Gay, E.J., Fedrigo, O., Lowe, C.G., Skomal, G., Cliff, G., Padilla, M.H., Huveneers, C., Lyons, K., Sato, K., Glancy, J., Lesturgie, P., Mona, S., and Naylor, G.J.P. (2025). A genomic test of sex-biased dispersal in white sharks. Proceedings of the National Academy of Sciences 122, e2507931122. https://doi.org/10.1073/pnas.2507931122.

56. Le Cam, S., Brémaud, J., Becquet, V., Huet, V., Dubillot, E., Garcia, P., Viricel, A., Breton, S., and Pante, E. (2025). Discordant population structure inferred from male- and female-type mtDNAs from Macoma balthica, a bivalve species characterized by doubly uniparental inheritance of mitochondria. Peer Community Journal 5, e29. https://doi.org/10.24072/pcjournal.529.

57. Le Cosquer, G., Pannier, M., Meunier, E., Thevenin, J., Pyhourquet, E., Guyonnet, S., Vellas, B., Santin, Y., Guiard, B., Parini, A., Buscail, L., Bournet, B., Guillemet, D., Deraison, C., Vergnolle, N., Motta, J.-P., and for the IHU HealthAge INSPIRE/Open Science study group (2025). Pathogenicity of commensal gut biofilm in prefrail aging. npj Biofilms and Microbiomes 11, 84. https://doi.org/10.1038/s41522-025-00716-8.

58. Leclerc, L., Agoutin, G., Brévault, T., Champion, A., Mainguy, J., Nègre, N., Yainna, S., Pascal, G., Gaudriault, S., and Ogier, J.-C. (2025). Nested PCR to optimize rpoB metabarcoding for low-concentration and host-associated bacterial DNA. Microbiology Spectrum 13, e01417–25. https://doi.org/10.1128/spectrum.01417-25.

59. Lemarcis, T., Blin, A., Cariou, M., Derzelle, A., Farhat, S., Fedosov, A., Zaharias, P., Zuccon, D., and Puillandre, N. (2025). Too Far From Relatives? Impact of the Genetic Distance on the Success of Exon Capture in Phylogenomics. Molecular Ecology Resources 25, e14064. https://doi.org/10.1111/1755-0998.14064.

60. Leroy, T., Albert, E., Thouroude, T., Baudino, S., Caissard, J.-C., Chastellier, A., Chameau, J., Jeauffre, J., Loubert, T., Nindya Paramita, S., Pernet, A., Soufflet-Freslon, V., Oghina-Pavie, C., Foucher, F., Hibrand-Saint Oyant, L., and Clotault, J. (2025). Dark side of the honeymoon: Reconstructing the Asian × European rose breeding history through the lens of genomics. GENETICS 231, iyaf163. https://doi.org/10.1093/genetics/iyaf163.

61. Lesturgie, P., Denton, J.S.S., Yang, L., Corrigan, S., Kneebone, J., Laso-Jadart, R., Lynghammar, A., Fedrigo, O., Mona, S., and Naylor, G.J.P. (2025). Short-term evolutionary implications of an introgressed size-determining supergene in a vulnerable population. Nature Communications 16, 1096. https://doi.org/10.1038/s41467-025-56126-z.

62. Loupit, G., Valls Fonayet, J., Tran, J., Garcia, V., Hummel, I., Petriacq, P., Gallusci, P., Berger, M., Franc, C., De Revel, G., Ollat, N., and Cookson, S.J. (2025). Graft union formation involves interactions among bud signals, carbon availability, dormancy release, wound responses and non‐self‐communication in grapevine. The Plant Journal 122, e70244. https://doi.org/10.1111/tpj.70244.

63. Malonga, T., Knudsen, C., Alberge, J., Lhuillier, E., Aymard, P., Jones, E., Lencina, C., Despeyroux, M., Riant, E., Cabau, C., Ivy, A., Loving, C.L., Vialaneix, N., and Beaumont, M. (2026). A Single-Cell Atlas of Transcriptome Changes in the Intestinal Epithelium at the Suckling-to-Weaning Transition in Male Rabbits. Cellular and Molecular Gastroenterology and Hepatology 20, 101628. https://doi.org/10.1016/j.jcmgh.2025.101628.

64. Marchaud, E., Morin, R., Iacovoni, J.S., Draia-Nicolau, T., Gomes, A., Norlund, M., Bernes-Lasserre, P., Lagarde, J.-M., Prats, A.-C., Garmy-Susini, B., Bouloumie, A., Briot, A., and Tatin, F. (2025). 3D imaging and single-cell analysis reveal cellular heterogeneity of lymphatic valve endothelial cell types. iScience 28, 113841. https://doi.org/10.1016/j.isci.2025.113841.

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