BiRD bioinformatics Hub

Publications

2025

Authored

    Acknowledged

    1. Champion, O., Maïga, S., Antier, C., Dousset, C., Moreau-Aubry, A., Bellanger, C., Guillonneau, F., Descamps, G., Moreno, J. A., Kwon, O., Lilli, N. L., Moreau, P., Chiron, D., Pellat-Deceunynck, C., Touzeau, C., & Gomez-Bougie, P. (2025). VDAC2 primes myeloma cells for BAK-dependent apoptosis and represents a novel therapeutic target. Leukemia. Acknowledged. https://doi.org/10.1038/s41375-025-02523-8 https://doi.org/10.1038/s41375-025-02523-8
    2. Souazé, F., Lefebvre, C., Giowachini, P., Derrien, J., Naour, M., Corre, I., Douillard, E., Guillonneau, F., Campone, M., & Juin, P. (2025). MCL-1 as a molecular switch between myofibroblastic and pro-angiogenic features of breast cancer- associated fibroblasts. Acknowledged. https://doi.org/10.21203/rs.3.rs-6007010/v1 https://doi.org/10.21203/rs.3.rs-6007010/v1
    3. Zhang, B., Rimbert, A., Lainé, A., Huijkman, N., Kloosterhuis, N., Smit, M., van de Sluis, B., Kuivenhoven, J. A., & Tharehalli, U. (2025). A study into rare GPR146 gene variants in humans and mice. Atherosclerosis, 119137. https://doi.org/10.1016/j.atherosclerosis.2025.119137 https://doi.org/10.1016/j.atherosclerosis.2025.119137
    4. Ramondenc, S., Eveillard, D., Metfies, K., Iversen, M. H., Nöthig, E.-M., Piepenburg, D., Hasemann, C., & Soltwedel, T. (2025). Unveiling pelagic-benthic coupling associated with the biological carbon pump in the Fram Strait (Arctic Ocean). Nature Communications, 16(1). https://doi.org/10.1038/s41467-024-55221-x https://doi.org/10.1038/s41467-024-55221-x
    5. Manirakiza, E., Chaumier, T., & Tirichine, L. (2025). Complete genome sequence of a marine Pseudoalteromonas bacterial strain. Microbiology Resource Announcements, 14(1). https://doi.org/10.1128/mra.00975-24 https://doi.org/10.1128/mra.00975-24
    6. Cardon, A., Guinebretière, T., Dong, C., Gil, L., Ado, S., Gavlovsky, P.-jean, Braud, M., Danger, R., Schultheiß, C., Doméné, A., Paul-Gilloteaux, P., Chevalier, C., Bernier, L., Judor, J.-P., Fourgeux, C., Imbert, A., Khaldi, M., Bardou-Jacquet, E., Elkrief, L., … Renand, A. (2025). Single cell profiling of circulating autoreactive CD4 T cells from patients with autoimmune liver diseases suggests tissue imprinting. Nature Communications, 16(1). https://doi.org/10.1038/s41467-025-56363-2 https://doi.org/10.1038/s41467-025-56363-2
    7. Cardon, A., Guinebretière, T., Dong, C., Gil, L., Ado, S., Gavlovsky, P.-jean, Braud, M., Danger, R., Schultheiß, C., Doméné, A., Paul-Gilloteaux, P., Chevalier, C., Bernier, L., Judor, J.-P., Fourgeux, C., Imbert, A., Khaldi, M., Bardou-Jacquet, E., Elkrief, L., … Renand, A. (2025). Single cell profiling of circulating autoreactive CD4 T cells from patients with autoimmune liver diseases suggests tissue imprinting. Nature Communications, 16(1). https://doi.org/10.1038/s41467-025-56363-2 https://doi.org/10.1038/s41467-025-56363-2

    2024

    Authored

    1. Lamarre, P., Andersen, J., Gaignard, A., & Cazalens, S. (2024, November). A generic framework to better understand and compare FAIRness measures. Knowledge Engineering and Knowledge Management - 24rd International Conference, EKAW 2024. https://hal.science/hal-04709107 http://hal.inria.fr/hal-04709107
    2. Gaignard, A., Tsueng, G., Mičetić, I., Castro, L. J., & Juty, N. (2024). Improving Bioschemas creation and community adoption through process improvements, tool development, and advancing compliance to FAIR standards. https://doi.org/10.37044/osf.io/8km9j https://doi.org/10.37044/osf.io/8km9j

    Acknowledged

    1. Soueidan, A., Idiri, K., Becchina, C., Esparbès, P., Legrand, A., Le Bastard, Q., & Montassier, E. (2024). Pooled analysis of oral microbiome profiles defines robust signatures associated with periodontitis. MSystems, 9(11). https://doi.org/10.1128/msystems.00930-24 https://doi.org/10.1128/msystems.00930-24
    2. Durand, R., Bellanger, C., Descamps, G., Dousset, C., Maïga, S., Derrien, J., Thirouard, L., Bouard, L., Asnagli, H., Beer, P., Parker, A., Gomez‐Bougie, P., Devilder, M. C., Moreau, P., Touzeau, C., Moreau‐Aubry, A., Chiron, D., & Pellat‐Deceunynck, C. (2024). Combined inhibition of CTPS1 and ATR is a metabolic vulnerability in p53‐deficient myeloma cells. HemaSphere, 8(10). https://doi.org/10.1002/hem3.70016 https://doi.org/10.1002/hem3.70016
    3. Manirakiza, E., Chaumier, T., & Tirichine, L. (2024). Genomic sequences and annotations of two Pseudomonas species isolated from marine and terrestrial habitats. Microbiology Resource Announcements, 13(10). https://doi.org/10.1128/mra.00373-24 https://doi.org/10.1128/mra.00373-24
    4. Manirakiza, E., Chaumier, T., & Tirichine, L. (2024). Genomic sequences and annotations of two Pseudomonas species isolated from marine and terrestrial habitats. Microbiology Resource Announcements, 13(10). https://doi.org/10.1128/mra.00373-24 https://doi.org/10.1128/mra.00373-24
    5. Demuth, S., Faddeenkov, I., Paris, J., Rousseau, O., Baciotti, B., Payet, M., Casey, R., Vukusic, S., Doyle, S., Jarre, G., Vince, N., Limou, S., Sèze, J. D., Kerbrat, A., Laplaud, D., Edan, G., & Gourraud, P.-A. (2024). Are we in a Big Data era for multiple sclerosis? Lessons from integrating clinical trials and observational studies data into the PRIMUS precision medicine platform. Acknowledged. https://doi.org/10.1101/2024.10.17.24315655 https://doi.org/10.1101/2024.10.17.24315655
    6. Durand, R., Bellanger, C., Descamps, G., Dousset, C., Maïga, S., Derrien, J., Thirouard, L., Bouard, L., Asnagli, H., Beer, P., Parker, A., Gomez‐Bougie, P., Devilder, M. C., Moreau, P., Touzeau, C., Moreau‐Aubry, A., Chiron, D., & Pellat‐Deceunynck, C. (2024). Combined inhibition of CTPS1 and ATR is a metabolic vulnerability in p53‐deficient myeloma cells. HemaSphere, 8(10). https://doi.org/10.1002/hem3.70016 https://doi.org/10.1002/hem3.70016
    7. Manirakiza, E., Chaumier, T., & Tirichine, L. (2024). Genomic sequences and annotations of two Pseudomonas species isolated from marine and terrestrial habitats. Microbiology Resource Announcements, 13(10). https://doi.org/10.1128/mra.00373-24 https://doi.org/10.1128/mra.00373-24
    8. Bhattacharya, N., Rockstroh, A., Deshpande, S. S., Thomas, S. K., Yadav, A., Goswami, C., Chawla, S., Solomon, P., Fourgeux, C., Ahuja, G., Hollier, B. G., Kumar, H., Roquilly, A., Poschmann, J., Lehman, M., Nelson, C. C., & Sengupta, D. (2024). Pseudo-grading of tumor subpopulations from single-cell transcriptomic data using Phenotype Algebra. Acknowledged. https://doi.org/10.7554/elife.98469.1 https://doi.org/10.7554/elife.98469.1
    9. Brocard, S., Morin, M., dos Santos Brito Silva, N., Renaud-Picard, B., Coiffard, B., Demant, X., Falque, L., Le Pavec, J., Roux, A., Villeneuve, T., Knoop, C., Mornex, J.-F., Salpin, M., Boussaud, V., Rousseau, O., Mauduit, V., Durand, A., Magnan, A., Gourraud, P.-A., … Le Pavec, J. (2024). Description and first insights on a large genomic biobank of lung transplantation. European Journal of Human Genetics. Acknowledged. https://doi.org/10.1038/s41431-024-01683-y https://doi.org/10.1038/s41431-024-01683-y
    10. Alves, I., Giemza, J., Blum, M. G. B., Bernhardsson, C., Chatel, S., Karakachoff, M., Saint Pierre, A., Herzig, A. F., Olaso, R., Monteil, M., Gallien, V., Cabot, E., Svensson, E., Bacq, D., Baron, E., Berthelier, C., Besse, C., Blanché, H., Bocher, O., … Dina, C. (2024). Human genetic structure in Northwest France provides new insights into West European historical demography. Nature Communications, 15(1). https://doi.org/10.1038/s41467-024-51087-1 https://doi.org/10.1038/s41467-024-51087-1
    11. Alves, I., Giemza, J., Blum, M. G. B., Bernhardsson, C., Chatel, S., Karakachoff, M., Saint Pierre, A., Herzig, A. F., Olaso, R., Monteil, M., Gallien, V., Cabot, E., Svensson, E., Bacq, D., Baron, E., Berthelier, C., Besse, C., Blanché, H., Bocher, O., … Dina, C. (2024). Human genetic structure in Northwest France provides new insights into West European historical demography. Nature Communications, 15(1). https://doi.org/10.1038/s41467-024-51087-1 https://doi.org/10.1038/s41467-024-51087-1
    12. Chatelain, C., Berland, L., Grard, M., Jouand, N., Fresquet, J., Nader, J., Hirigoyen, U., Petithomme, T., Combredet, C., Pons-Tostivint, E., Fradin, D., Treps, L., Blanquart, C., Boisgerault, N., Tangy, F., & Fonteneau, J.-F. (2024). Interplay between oncolytic measles virus, macrophages and cancer cells induces a proinflammatory tumor microenvironment. OncoImmunology, 13(1). https://doi.org/10.1080/2162402x.2024.2377830 https://doi.org/10.1080/2162402x.2024.2377830
    13. Michenaud, L., Marrié, N., Rimbert, A., Marmontel, O., Charrière, S., Gibert, C., Bouveyron, C., Mammi, J., Cariou, B., Moulin, P., & Di Filippo, M. (2024). Evaluation of biochemical algorithms to screen dysbetalipoproteinemia in ε2ε2 and rare APOE variants carriers. Clinical Chemistry and Laboratory Medicine (CCLM). Acknowledged. https://doi.org/10.1515/cclm-2024-0587 https://doi.org/10.1515/cclm-2024-0587
    14. Gaudin, M., Eveillard, D., & Chaffron, S. (2024). Ecological associations distribution modelling of marine plankton at a global scale. Philosophical Transactions of the Royal Society B: Biological Sciences, 379(1909). https://doi.org/10.1098/rstb.2023.0169 https://doi.org/10.1098/rstb.2023.0169
    15. Mozin, E., Massouridès, E., Mournetas, V., Lièvre, C., Bourdon, A., Jackson, D. L., Packer, J. S., Seong, J., Trapnell, C., Le Guiner, C., Adjali, O., Pinset, C., Mack, D. L., & Dupont, J.-B. (2024). Dystrophin deficiency impairs cell junction formation during embryonic myogenesis from pluripotent stem cells. IScience, 27(7), 110242. https://doi.org/10.1016/j.isci.2024.110242 https://doi.org/10.1016/j.isci.2024.110242
    16. Sailliet, N., Dupuy, A., Brinas, F., Renaudin, K., Colas, L., Kerleau, C., Nguyen, T.-V.-H., Fourgeux, C., Poschmann, J., Gosset, C., Giral, M., Degauque, N., Mai, H. L., Danger, R., & Brouard, S. (2024). Regulatory B Cells Expressing Granzyme B from Tolerant Renal Transplant Patients: Highly Differentiated B Cells with a Unique Pathway with a Specific Regulatory Profile and Strong Interactions with Immune System Cells. Cells, 13(15), 1287. https://doi.org/10.3390/cells13151287 https://doi.org/10.3390/cells13151287
    17. Mozin, E., Massouridès, E., Mournetas, V., Lièvre, C., Bourdon, A., Jackson, D. L., Packer, J. S., Seong, J., Trapnell, C., Le Guiner, C., Adjali, O., Pinset, C., Mack, D. L., & Dupont, J.-B. (2024). Dystrophin deficiency impairs cell junction formation during embryonic myogenesis from pluripotent stem cells. IScience, 27(7), 110242. https://doi.org/10.1016/j.isci.2024.110242 https://doi.org/10.1016/j.isci.2024.110242
    18. Sailliet, N., Dupuy, A., Brinas, F., Renaudin, K., Colas, L., Kerleau, C., Nguyen, T.-V.-H., Fourgeux, C., Poschmann, J., Gosset, C., Giral, M., Degauque, N., Mai, H. L., Danger, R., & Brouard, S. (2024). Regulatory B Cells Expressing Granzyme B from Tolerant Renal Transplant Patients: Highly Differentiated B Cells with a Unique Pathway with a Specific Regulatory Profile and Strong Interactions with Immune System Cells. Cells, 13(15), 1287. https://doi.org/10.3390/cells13151287 https://doi.org/10.3390/cells13151287
    19. Geryk, M., Canac, R., Forest, V., Lindenbaum, P., Girardeau, A., Baudic, M., Baron, E., Bibonne, A., Chariau, C., Kyndt, F., Redon, R., Schott, J.-J., Gourraud, J.-B., Barc, J., & Charpentier, F. (2024). Generation of a patient-specific induced pluripotent stem cell line carrying the DES p.R406W mutation, an isogenic control and a DES p.R406W knock-in line. Stem Cell Research, 77, 103396. https://doi.org/10.1016/j.scr.2024.103396 https://doi.org/10.1016/j.scr.2024.103396
    20. Lamirault, G., Fellah-Hebia, I., Chevalier, C., Guisle, I., Guyomarc’h, B., Solnon, A., Gourraud, J.-B., Desprets, L., Abbey, S., Leclercq, C., Bru, P., Milhem, A., Billon, O., Anselme, F., Savouré, A., Trochu, J.-N., Houlgatte, R., Lande, G., & Steenman, M. (2024). The cardiac blood transcriptome predicts de novo onset of atrial fibrillation in heart failure. Journal of Molecular and Cellular Cardiology Plus, 8, 100077. https://doi.org/10.1016/j.jmccpl.2024.100077 https://doi.org/10.1016/j.jmccpl.2024.100077
    21. Lamirault, G., Fellah-Hebia, I., Chevalier, C., Guisle, I., Guyomarc’h, B., Solnon, A., Gourraud, J.-B., Desprets, L., Abbey, S., Leclercq, C., Bru, P., Milhem, A., Billon, O., Anselme, F., Savouré, A., Trochu, J.-N., Houlgatte, R., Lande, G., & Steenman, M. (2024). The cardiac blood transcriptome predicts de novo onset of atrial fibrillation in heart failure. Journal of Molecular and Cellular Cardiology Plus, 8, 100077. https://doi.org/10.1016/j.jmccpl.2024.100077 https://doi.org/10.1016/j.jmccpl.2024.100077
    22. Renoult, O., Laurent–Blond, M., Awada, H., Oliver, L., Joalland, N., Croyal, M., Paris, F., Gratas, C., & Pecqueur, C. (2024). Metabolic profiling of glioblastoma stem cells reveals pyruvate carboxylase as a critical survival factor and potential therapeutic target. Neuro-Oncology, 26(9), 1572–1586. https://doi.org/10.1093/neuonc/noae106 https://doi.org/10.1093/neuonc/noae106
    23. Lamirault, G., Fellah-Hebia, I., Chevalier, C., Guisle, I., Guyomarc’h, B., Solnon, A., Gourraud, J.-B., Desprets, L., Abbey, S., Leclercq, C., Bru, P., Milhem, A., Billon, O., Anselme, F., Savouré, A., Trochu, J.-N., Houlgatte, R., Lande, G., & Steenman, M. (2024). The cardiac blood transcriptome predicts de novo onset of atrial fibrillation in heart failure. Journal of Molecular and Cellular Cardiology Plus, 8, 100077. https://doi.org/10.1016/j.jmccpl.2024.100077 https://doi.org/10.1016/j.jmccpl.2024.100077
    24. Renoult, O., Laurent–Blond, M., Awada, H., Oliver, L., Joalland, N., Croyal, M., Paris, F., Gratas, C., & Pecqueur, C. (2024). Metabolic profiling of glioblastoma stem cells reveals pyruvate carboxylase as a critical survival factor and potential therapeutic target. Neuro-Oncology, 26(9), 1572–1586. https://doi.org/10.1093/neuonc/noae106 https://doi.org/10.1093/neuonc/noae106
    25. Jézéquel, P., Lasla, H., Gouraud, W., Basseville, A., Michel, B., Frenel, J.-S., Juin, P. P., Ben Azzouz, F., & Campone, M. (2024). Mesenchymal-like immune-altered is the fourth robust triple-negative breast cancer molecular subtype. Breast Cancer. Acknowledged. https://doi.org/10.1007/s12282-024-01597-z https://doi.org/10.1007/s12282-024-01597-z
    26. Onfray, C., Chevolleau, S., Moinard, E., Girard, O., Mahadik, K., Allsop, R., Georgolopoulos, G., Lavigne, R., Renoult, O., Aksoy, I., Lemaitre, E., Hulin, P., Ouimette, J.-F., Fréour, T., Pecqueur, C., Pineau, C., Pasque, V., Rougeulle, C., & David, L. (2024). Unraveling hallmark suitability for staging pre- and post-implantation stem cell models. Cell Reports, 43(5), 114232. https://doi.org/10.1016/j.celrep.2024.114232 https://doi.org/10.1016/j.celrep.2024.114232
    27. Bolteau, M., Chebouba, L., David, L., Bourdon, J., & Guziolowski, C. (2024). Boolean Network Models of Human Preimplantation Development. Journal of Computational Biology. Acknowledged. https://doi.org/10.1089/cmb.2024.0517 https://doi.org/10.1089/cmb.2024.0517
    28. Poschmann, J., Solomon, P., Kaurani, L., Budde, M., Guiné, J.-B., Krüger, D., Centeno, T., Burkhardt, S., Fourgeux, C., Adorjan, K., Heilbronner, M., Kalman, J., Kohshour, M. O., Papiol, S., Reich-Erkelenz, D., Schaupp, S., Schulte, E., Senner, F., Vogl, T., … Heilbronner, U. (2024). Integrative Analysis of miRNA Expression Profiles Reveals Distinct and Common Molecular Mechanisms Underlying Broad Diagnostic Groups of Severe Mental Disorders. Acknowledged. https://doi.org/10.21203/rs.3.rs-4279982/v1 https://doi.org/10.21203/rs.3.rs-4279982/v1
    29. Ishikawa, T., Masuda, T., Hachiya, T., Dina, C., Simonet, F., Nagata, Y., Tanck, M. W. T., Sonehara, K., Glinge, C., Tadros, R., Khongphatthanayothin, A., Lu, T.-P., Higuchi, C., Nakajima, T., Hayashi, K., Aizawa, Y., Nakano, Y., Nogami, A., Morita, H., … Makita, N. (2024). Brugada syndrome in Japan and Europe: a genome-wide association study reveals shared genetic architecture and new risk loci. European Heart Journal, 45(26), 2320–2332. https://doi.org/10.1093/eurheartj/ehae251 https://doi.org/10.1093/eurheartj/ehae251
    30. Ishikawa, T., Masuda, T., Hachiya, T., Dina, C., Simonet, F., Nagata, Y., Tanck, M. W. T., Sonehara, K., Glinge, C., Tadros, R., Khongphatthanayothin, A., Lu, T.-P., Higuchi, C., Nakajima, T., Hayashi, K., Aizawa, Y., Nakano, Y., Nogami, A., Morita, H., … Makita, N. (2024). Brugada syndrome in Japan and Europe: a genome-wide association study reveals shared genetic architecture and new risk loci. European Heart Journal, 45(26), 2320–2332. https://doi.org/10.1093/eurheartj/ehae251 https://doi.org/10.1093/eurheartj/ehae251
    31. Hulo, P., Deshayes, S., Fresquet, J., Chéné, A.-L., Blandin, S., Boisgerault, N., Fonteneau, J.-F., Treps, L., Denis, M. G., Bennouna, J., Fradin, D., Pons-Tostivint, E., & Blanquart, C. (2024). Use of non-small cell lung cancer multicellular tumor spheroids to study the impact of chemotherapy. Respiratory Research, 25(1). https://doi.org/10.1186/s12931-024-02791-5 https://doi.org/10.1186/s12931-024-02791-5
    32. Hervé, J., Haurogné, K., Allard, M., Sourice, S., Lindenbaum, P., Bach, J.-M., & Lieubeau, B. (2024). Spontaneous Akt2 deficiency in a colony of NOD mice exhibiting early diabetes. Scientific Reports, 14(1). https://doi.org/10.1038/s41598-024-60021-w https://doi.org/10.1038/s41598-024-60021-w
    33. Broquet, A., Gourain, V., Goronflot, T., Le Mabecque, V., Sinha, D., Ashayeripanah, M., Jacqueline, C., Martin, P., Davieau, M., Boutin, L., Poulain, C., Martin, F. P., Fourgeux, C., Petrier, M., Cannevet, M., Leclercq, T., Guillonneau, M., Chaumette, T., Laurent, T., … Roquilly, A. (2024). Sepsis-trained macrophages promote antitumoral tissue-resident T cells. Nature Immunology, 25(5), 802–819. https://doi.org/10.1038/s41590-024-01819-8 https://doi.org/10.1038/s41590-024-01819-8
    34. Ishnaiwer, M., Le Bastard, Q., Naour, M., Zeman, M., Dailly, E., Montassier, E., Batard, E., & Dion, M. (2024). Efficacy of an inulin-based treatment on intestinal colonization by multidrug-resistant E. coli: insight into the mechanism of action. Gut Microbes, 16(1). https://doi.org/10.1080/19490976.2024.2347021 https://doi.org/10.1080/19490976.2024.2347021
    35. Baudic, M., Murata, H., Bosada, F. M., Melo, U. S., Aizawa, T., Lindenbaum, P., van der Maarel, L. E., Guedon, A., Baron, E., Fremy, E., Foucal, A., Ishikawa, T., Ushinohama, H., Jurgens, S. J., Choi, S. H., Kyndt, F., Le Scouarnec, S., Wakker, V., Thollet, A., … Barc, J. (2024). TAD boundary deletion causes PITX2-related cardiac electrical and structural defects. Nature Communications, 15(1). https://doi.org/10.1038/s41467-024-47739-x https://doi.org/10.1038/s41467-024-47739-x
    36. Turpin, M., Madigou, T., Bizot, M., Acker, R., Avner, S., Benoit, G., Braud, M., Fourgeux, C., Palierne, G., Poschmann, J., Sawvell, K., Watrin, E., Le Peron, C., & Salbert, G. (2024). TDG orchestrates ATF4-dependent gene transcription during retinoic acid-induced cell fate acquisition. Acknowledged. https://doi.org/10.1101/2024.04.01.587571 https://doi.org/10.1101/2024.04.01.587571
    37. Baudic, M., Murata, H., Bosada, F. M., Melo, U. S., Aizawa, T., Lindenbaum, P., van der Maarel, L. E., Guedon, A., Baron, E., Fremy, E., Foucal, A., Ishikawa, T., Ushinohama, H., Jurgens, S. J., Choi, S. H., Kyndt, F., Le Scouarnec, S., Wakker, V., Thollet, A., … Barc, J. (2024). TAD boundary deletion causes PITX2-related cardiac electrical and structural defects. Nature Communications, 15(1). https://doi.org/10.1038/s41467-024-47739-x https://doi.org/10.1038/s41467-024-47739-x
    38. Turpin, M., Madigou, T., Bizot, M., Acker, R., Avner, S., Benoît, G., Braud, M., Fourgeux, C., Palierne, G., Poschmann, J., Sawvell, K., Watrin, E., Péron, C. L., & Salbert, G. (2024). TDG orchestrates ATF4-dependent gene transcription during retinoic acid-induced cell fate acquisition. Acknowledged. https://doi.org/10.1101/2024.04.01.587571 https://doi.org/10.1101/2024.04.01.587571
    39. Roudaut, M., Caillaud, A., Souguir, Z., Bray, L., Girardeau, A., Rimbert, A., Croyal, M., Lambert, G., Patitucci, M., Delpouve, G., Vandenhaute, É., Le May, C., Maubon, N., Cariou, B., & Si‐Tayeb, K. (2024). Human induced pluripotent stem cells‐derived liver organoids grown on a Biomimesys® hyaluronic acid‐based hydroscaffold as a new model for studying human lipoprotein metabolism. Bioengineering &Amp; Translational Medicine. Acknowledged. https://doi.org/10.1002/btm2.10659 https://doi.org/10.1002/btm2.10659
    40. Giordano, N., Gaudin, M., Trottier, C., Delage, E., Nef, C., Bowler, C., & Chaffron, S. (2024). Genome-scale community modelling reveals conserved metabolic cross-feedings in epipelagic bacterioplankton communities. Nature Communications, 15(1). https://doi.org/10.1038/s41467-024-46374-w https://doi.org/10.1038/s41467-024-46374-w
    41. Roudaut, M., Caillaud, A., Souguir, Z., Bray, L., Girardeau, A., Rimbert, A., Croyal, M., Lambert, G., Patitucci, M., Delpouve, G., Vandenhaute, É., Le May, C., Maubon, N., Cariou, B., & Si‐Tayeb, K. (2024). Human induced pluripotent stem cells‐derived liver organoids grown on a Biomimesys® hyaluronic acid‐based hydroscaffold as a new model for studying human lipoprotein metabolism. Bioengineering &Amp; Translational Medicine, 9(4). https://doi.org/10.1002/btm2.10659 https://doi.org/10.1002/btm2.10659
    42. Cardon, A., Guinebretière, T., Dong, C., Gil, L., Ado, S., Gavlovsky, P.-jean, Braud, M., Danger, R., Schultheiß, C., Doméné, A., Paul-Gilloteaux, P., Chevalier, C., Bernier, L., Judor, J.-P., Fourgeux, C., Imbert, A., Khaldi, M., Bardou-Jacquet, E., Elkrief, L., … Renand, A. (2024). The immune profile of circulating autoreactive CD4 T cells is imprinted through tissue activation during autoimmune liver diseases. Acknowledged. https://doi.org/10.1101/2024.03.26.586770 https://doi.org/10.1101/2024.03.26.586770
    43. Roudaut, M., Caillaud, A., Souguir, Z., Bray, L., Girardeau, A., Rimbert, A., Croyal, M., Lambert, G., Patitucci, M., Delpouve, G., Vandenhaute, É., Le May, C., Maubon, N., Cariou, B., & Si‐Tayeb, K. (2024). Human induced pluripotent stem cells‐derived liver organoids grown on a Biomimesys® hyaluronic acid‐based hydroscaffold as a new model for studying human lipoprotein metabolism. Bioengineering &Amp; Translational Medicine, 9(4). https://doi.org/10.1002/btm2.10659 https://doi.org/10.1002/btm2.10659
    44. Roudaut, M., Caillaud, A., Souguir, Z., Bray, L., Girardeau, A., Rimbert, A., Croyal, M., Lambert, G., Patitucci, M., Delpouve, G., Vandenhaute, É., Le May, C., Maubon, N., Cariou, B., & Si‐Tayeb, K. (2024). Human induced pluripotent stem cells‐derived liver organoids grown on a Biomimesys® hyaluronic acid‐based hydroscaffold as a new model for studying human lipoprotein metabolism. Bioengineering &Amp; Translational Medicine, 9(4). https://doi.org/10.1002/btm2.10659 https://doi.org/10.1002/btm2.10659
    45. Cardon, A., Guinebretière, T., Dong, C., Gil, L., Ado, S., Gavlovsky, P.-jean, Braud, M., Danger, R., Schultheiß, C., Doméné, A., Paul-Gilloteaux, P., Chevalier, C., Bernier, L., Judor, J.-P., Fourgeux, C., Imbert, A., Khaldi, M., Bardou-Jacquet, E., Elkrief, L., … Renand, A. (2024). The immune profile of circulating autoreactive CD4 T cells is imprinted through tissue activation during autoimmune liver diseases. Acknowledged. https://doi.org/10.1101/2024.03.26.586770 https://doi.org/10.1101/2024.03.26.586770
    46. Wargny, M., Goronflot, T., Rimbert, A., Boursier, J., Kab, S., Henny, J., Lainé, A., Leux, C., Smati, S., Hadjadj, S., Le May, C., Goldberg, M., Zins, M., & Cariou, B. (2024). Primary hypocholesterolemia is associated with an increased risk of hepatic complications in the general population. Journal of Hepatology. Acknowledged. https://doi.org/10.1016/j.jhep.2024.01.030 https://doi.org/10.1016/j.jhep.2024.01.030
    47. Durand, R., Bellanger, C., Kervoëlen, C., Tessoulin, B., Dousset, C., Menoret, E., Asnagli, H., Parker, A., Beer, P., Pellat-Deceunynck, C., & Chiron, D. (2024). Selective pharmacologic targeting of CTPS1 shows single-agent activity and synergizes with BCL2 inhibition in aggressive mantle cell lymphoma. Haematologica. Acknowledged. https://doi.org/10.3324/haematol.2023.284345 https://doi.org/10.3324/haematol.2023.284345
    48. Durand, R., Bellanger, C., Kervoëlen, C., Tessoulin, B., Dousset, C., Menoret, E., Asnagli, H., Parker, A., Beer, P., Pellat-Deceunynck, C., & Chiron, D. (2024). Selective pharmacologic targeting of CTPS1 shows single-agent activity and synergizes with BCL2 inhibition in aggressive mantle cell lymphoma. Haematologica. Acknowledged. https://doi.org/10.3324/haematol.2023.284345 https://doi.org/10.3324/haematol.2023.284345
    49. Chaumier, T., Yang, F., Manirakiza, E., Ait-Mohamed, O., Wu, Y., Chandola, U., Jesus, B., Piganeau, G., Groisillier, A., & Tirichine, L. (2024). Genome-wide assessment of genetic diversity and transcript variations in 17 accessions of the model diatom Phaeodactylum tricornutum. ISME Communications, 4(1). https://doi.org/10.1093/ismeco/ycad008 https://doi.org/10.1093/ismeco/ycad008
    50. Chaumier, T., Yang, F., Manirakiza, E., Ait-Mohamed, O., Wu, Y., Chandola, U., Jesus, B., Piganeau, G., Groisillier, A., & Tirichine, L. (2024). Genome-wide assessment of genetic diversity and transcript variations in 17 accessions of the model diatom Phaeodactylum tricornutum. ISME Communications, 4(1). https://doi.org/10.1093/ismeco/ycad008 https://doi.org/10.1093/ismeco/ycad008

    2023

    Authored

    1. Gaignard, A., Rosnet, T., de Lamotte, F., Lefort, V., & Devignes, M.-D. (2023). FAIR-Checker: supporting digital resource findability and reuse with Knowledge Graphs and Semantic Web standards. Journal of Biomedical Semantics, 14(1), 7. https://doi.org/10.1186/s13326-023-00289-5 https://doi.org/10.1186/s13326-023-00289-5 http://hal.inria.fr/hal-04148181
    2. Dang, M.-H., Gaignard, A., Skaf-Molli, H., & Molli, P. (2023, November). Schema.org : How is it used? International Semantic Web Conference (ISWC) 2023. https://hal.science/hal-04250523 http://hal.inria.fr/hal-04250523
    3. Sebe, C., Névéol, A., Cohen-Boulakia, S., & Gaignard, A. (2023). Extraction d’informations sur les workflows scientifiques à partir de la littérature. 23ème Conférence Francophone Sur l’Extraction Et La Gestion Des Connaissances (EGC), Extraction et Gestion des Connaissances, RNTI-E-39, 313–320. https://hal.science/hal-03991363 http://hal.inria.fr/hal-03991363
    4. Djaffardjy, M., Marchment, G., Sebe, C., Blanchet, R., Belhajjame, K., Gaignard, A., Lemoine, F., & Cohen-Boulakia, S. (2023). Developing and reusing bioinformatics data analysis pipelines using scientific workflow systems. Computational and Structural Biotechnology Journal, 21, 2075–2085. https://doi.org/https://doi.org/10.1016/j.csbj.2023.03.003 https://doi.org/https://doi.org/10.1016/j.csbj.2023.03.003

    Acknowledged

    1. Durand, R., Descamps, G., Dousset, C., Bellanger, C., Maïga, S., Alberge, J.-B., Derrien, J., Cruard, J., Minvielle, S., Lilli, N. L., GODON, C. A. T. H. E. R. I. N. E., Le Bris, Y., Tessoulin, B., Amiot, M., Gomez-Bougie, P., Touzeau, C., Moreau, P., Chiron, D., Moreau-Aubry, A., & Pellat-Deceunynck, C. (2023). A p53 score derived from TP53 CRISPR/Cas9 HMCLs predicts survival and reveals major role of BAX in BH3 mimetics response. Blood Journal. Acknowledged. https://doi.org/10.1182/blood.2023021581 https://doi.org/10.1182/blood.2023021581
    2. Montassier, E., Kitsios, G. D., Radder, J. E., Le Bastard, Q., Kelly, B. J., Panzer, A., Lynch, S. V., Calfee, C. S., Dickson, R. P., & Roquilly, A. (2023). Robust airway microbiome signatures in acute respiratory failure and hospital-acquired pneumonia. Nature Medicine, 29(11), 2793–2804. https://doi.org/10.1038/s41591-023-02617-9 https://doi.org/10.1038/s41591-023-02617-9
    3. Decombis, S., Bellanger, C., Le Bris, Y., Madiot, C., Jardine, J., Santos, J. C., Boulet, D., Dousset, C., Menard, A., Kervoelen, C., Douillard, E., Moreau, P., Minvielle, S., Moreau-Aubry, A., Tessoulin, B., Roue, G., Bidère, N., Le Gouill, S., Pellat-Deceunynck, C., & Chiron, D. (2023). CARD11 gain of function upregulates BCL2A1 expression and promotes resistance to targeted therapies combination in B-cell lymphoma. Blood, 142(18), 1543–1555. https://doi.org/10.1182/blood.2023020211 https://doi.org/10.1182/blood.2023020211
    4. Dekky, B., Azar, F., Bonnier, D., Monseur, C., Kalebić, C., Arpigny, E., Colige, A., Legagneux, V., & Théret, N. (2023). ADAMTS is a stromal modulator in chronic liver disease. The FASEB Journal, 37(11). https://doi.org/10.1096/fj.202200692rrrr https://doi.org/10.1096/fj.202200692rrrr
    5. Hendrix, S., Kingma, J., Ottenhoff, R., Valiloo, M., Svecla, M., Zijlstra, L. F., Sachdev, V., Kovac, K., Levels, J. H. M., Jongejan, A., de Boer, J. F., Kuipers, F., Rimbert, A., Norata, G. D., Loregger, A., & Zelcer, N. (2023). Hepatic SREBP signaling requires SPRING to govern systemic lipid metabolism in mice and humans. Nature Communications, 14(1). https://doi.org/10.1038/s41467-023-40943-1 https://doi.org/10.1038/s41467-023-40943-1
    6. Riquin, K., Isidor, B., Mercier, S., Nizon, M., Colin, E., Bonneau, D., Pasquier, L., Odent, S., Horn, X. M. L. G., Guyader, G. L., Toutain, A., Meyer, V., Deleuze, J.-F., Pichon, O., Doco-Fenzy, M., Bézieau, S., & Cogné, B. (2023). Integrating RNA-Seq into genome sequencing workflow enhances the analysis of structural variants causing neurodevelopmental disorders. Journal of Medical Genetics, jmg–2023–109263. https://doi.org/10.1136/jmg-2023-109263 https://doi.org/10.1136/jmg-2023-109263
    7. Bessonneau-Gaborit, V., Cruard, J., Guerin-Charbonnel, C., Derrien, J., Alberge, J.-B., Douillard, E., Devic, M., Deshayes, S., Campion, L., Westermann, F., Moreau, P., Herrmann, C., Bourdon, J., Magrangeas, F., & Minvielle, S. (2023). Exploring the impact of dexamethasone on gene regulation in myeloma cells. Life Science Alliance, 6(9), e202302195. https://doi.org/10.26508/lsa.202302195 https://doi.org/10.26508/lsa.202302195
    8. Martinez, L., Pouvreau, J.-B., Jestin, C., Montiel, G., Gravot, A., Berardocco, S., Marnet, N., Bouchereau, A., Delage, E., Simier, P., & Poulin, L. (2023). Comparative analysis of two neighboring conducive and suppressive soils towards plant parasitism caused by Phelipanche ramosa L. Pomel on Brassica napus L. Acknowledged. https://doi.org/10.21203/rs.3.rs-3059250/v1 https://doi.org/10.21203/rs.3.rs-3059250/v1
    9. Defois, A., Bon, N., Charpentier, A., Georget, M., Gaigeard, N., Blanchard, F., Hamel, A., Waast, D., Armengaud, J., Renoult, O., Pecqueur, C., Maugars, Y., Boutet, M.-A., Guicheux, J., & Vinatier, C. (2023). Osteoarthritic chondrocytes undergo a glycolysis-related metabolic switch upon exposure to IL-1b or TNF. Cell Communication and Signaling, 21(1). https://doi.org/10.1186/s12964-023-01150-z https://doi.org/10.1186/s12964-023-01150-z
    10. Vanhoye, X., Bardel, C., Rimbert, A., Moulin, P., Rollat-Farnier, P.-A., Muntaner, M., Marmontel, O., Dumont, S., Charrière, S., Cornélis, F., Ducluzeau, P. H., Fonteille, A., Nobecourt, E., Peretti, N., Schillo, F., Wargny, M., Cariou, B., Meirhaeghe, A., & Filippo, M. D. (2023). A new 165-SNP low-density lipoprotein cholesterol polygenic risk score based on next generation sequencing outperforms previously published scores in routine diagnostics of familial hypercholesterolemia. Translational Research, 255, 119–127. https://doi.org/10.1016/j.trsl.2022.12.002 https://doi.org/10.1016/j.trsl.2022.12.002
    11. Wu, Y., Chaumier, T., Manirakiza, E., Veluchamy, A., & Tirichine, L. (2023). PhaeoEpiView: an epigenome browser of the newly assembled genome of the model diatom Phaeodactylum tricornutum. Scientific Reports, 13(1). https://doi.org/10.1038/s41598-023-35403-1 https://doi.org/10.1038/s41598-023-35403-1
    12. Vanhoye, X., Bardel, C., Rimbert, A., Moulin, P., Rollat-Farnier, P.-A., Muntaner, M., Marmontel, O., Dumont, S., Charrière, S., Cornélis, F., Ducluzeau, P. H., Fonteille, A., Nobecourt, E., Peretti, N., Schillo, F., Wargny, M., Cariou, B., Meirhaeghe, A., & Filippo, M. D. (2023). A new 165-SNP low-density lipoprotein cholesterol polygenic risk score based on next generation sequencing outperforms previously published scores in routine diagnostics of familial hypercholesterolemia. Translational Research, 255, 119–127. https://doi.org/10.1016/j.trsl.2022.12.002 https://doi.org/10.1016/j.trsl.2022.12.002
    13. Maaziz, N., Garrec, C., Airaud, F., Bobée, V., Contentin, N., Cayssials, E., Rimbert, A., Aral, B., Bézieau, S., Gardie, B., & Girodon, F. (2023). Germline JAK2 E846D Substitution as the Cause of Erythrocytosis? Genes, 14(5), 1066. https://doi.org/10.3390/genes14051066 https://doi.org/10.3390/genes14051066
    14. Sinha, D., Laurent, T., Broquet, A., Fourgeux, C., Letellier, T., Tilly, G., Bruneau, S., Ville, S., Bouchet-Delbos, L., Brancherau, J., Kerleau, C., Brouard, S., Blancho, G., Giral, M., Josien, R., Danger, R., Roquilly, A., Degauque, N., & Poschmann, J. (2023). A Gene-expression Module Identifies Circulating Immune Cells with Enhanced Recruitment to Sites of Inflammation. Acknowledged. https://doi.org/10.1101/2023.04.11.536347 https://doi.org/10.1101/2023.04.11.536347
    15. Myasoedova, V. A., Rimbert, A., Camera, M., May, C. L., Capoulade, R., Cariou, B., & Poggio, P. (2023). LDL lowering effect of PCSK9 inhibition is reduced in women. European Heart Journal - Cardiovascular Pharmacotherapy, 9(4), 337–342. https://doi.org/10.1093/ehjcvp/pvad009 https://doi.org/10.1093/ehjcvp/pvad009
    16. Freneau, M., Blanchet, R., Benichi, S., Mrad, M.-A., Batta, S. P. R., Rio, M., Bonnaud, S., Lindenbaum, P., Laporte, F., Cuénot, S., Quillard, T., Morel, S., Kwak, B. R., Bijlenga, P., Deleuze, J.-F., Dina, C., Bodet, M., Chatel, S., Bourcereau, E., … Redon, R. (2023). Identification of rare missense variants reducing cathepsin O secretion in families with intracranial aneurysm. Acknowledged. https://doi.org/10.1101/2023.01.31.23285168 https://doi.org/10.1101/2023.01.31.23285168
    17. Freneau, M., Blanchet, R., Benichi, S., Mrad, M.-A., Batta, S. P. R., Rio, M., Bonnaud, S., Lindenbaum, P., Laporte, F., Cuénot, S., Quillard, T., Morel, S., Kwak, B. R., Bijlenga, P., Deleuze, J.-F., Dina, C., Bodet, M., Chatel, S., Bourcereau, E., … Redon, R. (2023). Identification of rare missense variants reducing cathepsin O secretion in families with intracranial aneurysm. Acknowledged. https://doi.org/10.1101/2023.01.31.23285168 https://doi.org/10.1101/2023.01.31.23285168
    18. Fizanne, L., Villard, A., Benabbou, N., Recoquillon, S., Soleti, R., Delage, E., Wertheimer, M., Vidal-Gómez, X., Oullier, T., Chaffron, S., Martı́nez M. Carmen, Neunlist, M., Boursier, J., & Andriantsitohaina, R. (2023). Faeces-derived extracellular vesicles participate in the onset of barrier dysfunction leading to liver diseases. Journal of Extracellular Vesicles, 12(2). https://doi.org/10.1002/jev2.12303 https://doi.org/10.1002/jev2.12303
    19. Lê, A., Selle, A., Aubert, P., Durand, T., Brosseau, C., Bordron, P., Delage, E., Chaffron, S., Petitfils, C., Cenac, N., Neunlist, M., Bodinier, M., & Rolli-Derkinderen, M. (2023). Maternal prebiotic supplementation impacts colitis development in offspring mice. Frontiers in Nutrition, 9. https://doi.org/10.3389/fnut.2022.988529 https://doi.org/10.3389/fnut.2022.988529
    20. Nguyen, N.-K., Devilder, M.-C., Gautreau-Rolland, L., Fourgeux, C., Sinha, D., Poschmann, J., Hourmant, M., Bressollette-Bodin, C., Saulquin, X., & McIlroy, D. (2023). A cluster of broadly neutralizing IgG against BK polyomavirus in a repertoire dominated by IgM. Life Science Alliance, 6(4), e202201567. https://doi.org/10.26508/lsa.202201567 https://doi.org/10.26508/lsa.202201567
    21. Dijoux, E., Klein, M., Misme-Aucouturier, B., Cheminant, M.-A., de Carvalho, M., Collin, L., Hassoun, D., Delage, E., Gourdel, M., Loirand, G., Sauzeau, V., Magnan, A., & Bouchaud, G. (2023). Allergic Sensitization Driving Immune Phenotyping and Disease Severity in a Mouse Model of Asthma. Allergy, Asthma &Amp\Mathsemicolon Immunology Research, 15(2), 246. https://doi.org/10.4168/aair.2023.15.2.246 https://doi.org/10.4168/aair.2023.15.2.246
    22. Bolteau, M., Bourdon, J., David, L., & Guziolowski, C. (2023). Inferring Boolean Networks from Single-Cell Human Embryo Datasets. In Lecture Notes in Computer Science (pp. 431–441). Springer Nature Singapore. https://doi.org/10.1007/978-981-99-7074-2_34 https://doi.org/10.1007/978-981-99-7074-2_34

    2022

    Authored

    1. Jotereau, F., Alameddine, J., Teusan, R., Pédron, A., Jouand, N., Altare, F., & Godefroy, E. (2022). Human gut microbiota-reactive DP8\upalpha regulatory T cells, signature and related emerging functions. Frontiers in Immunology, 13. https://doi.org/10.3389/fimmu.2022.1026994 https://doi.org/10.3389/fimmu.2022.1026994
    2. Churcheward, B., Millet, M., Bihouée, A., Fertin, G., & Chaffron, S. (2022). MAGNETO: An Automated Workflow for Genome-Resolved Metagenomics. MSystems, 7(4). https://doi.org/10.1128/msystems.00432-22 https://doi.org/10.1128/msystems.00432-22
    3. Dominguez-Huerta, G., Zayed, A. A., Wainaina, J. M., Guo, J., Tian, F., Pratama, A. A., Bolduc, B., Mohssen, M., Zablocki, O., Pelletier, E., Delage, E., Alberti, A., Aury, J.-M., Carradec, Q., da Silva, C., Labadie, K., Poulain, J., Bowler, C., Eveillard, D., … and, M. B. S. (2022). Diversity and ecological footprint of Global Ocean RNA viruses. Science, 376(6598), 1202–1208. https://doi.org/10.1126/science.abn6358 https://doi.org/10.1126/science.abn6358
    4. Zayed, A. A., Wainaina, J. M., Dominguez-Huerta, G., Pelletier, E., Guo, J., Mohssen, M., Tian, F., Pratama, A. A., Bolduc, B., Zablocki, O., Cronin, D., Solden, L., Delage, E., Alberti, A., Aury, J.-M., Carradec, Q., da Silva, C., Labadie, K., Poulain, J., … and, P. W. (2022). Cryptic and abundant marine viruses at the evolutionary origins of Earth’s RNA virome. Science, 376(6589), 156–162. https://doi.org/10.1126/science.abm5847 https://doi.org/10.1126/science.abm5847
    5. Misme-Aucouturier, B., Carvalho, M. D., Delage, E., Dijoux, E., Klein, M., Brosseau, C., Bodinier, M., Guzylack-Piriou, L., & Bouchaud, G. (2022). Oral exposure to bisphenol A exacerbates allergic inflammation in a mouse model of food allergy. Toxicology, 472, 153188. https://doi.org/10.1016/j.tox.2022.153188 https://doi.org/10.1016/j.tox.2022.153188
    6. Barc, J., Tadros, R., Glinge, C., Chiang, D. Y., Jouni, M., Simonet, F., Jurgens, S. J., Baudic, M., Nicastro, M., Potet, F., Offerhaus, J. A., Walsh, R., Choi, S. H., Verkerk, A. O., Mizusawa, Y., Anys, S., Minois, D., Arnaud, M., Duchateau, J., … and. (2022). Genome-wide association analyses identify new Brugada syndrome risk loci and highlight a new mechanism of sodium channel regulation in disease susceptibility. Nature Genetics, 54(3), 232–239. https://doi.org/10.1038/s41588-021-01007-6 https://doi.org/10.1038/s41588-021-01007-6
    7. Alves, I., Giemza, J., Blum, M., Bernhardsson, C., Chatel, S., Karakachoff, M., Pierre, A. S., Herzig, A. F., Olaso, R., Monteil, M., Gallien, V., Cabot, E., Svensson, E., Bacq-Daian, D., Baron, E., Berthelier, C., Besse, C., Blanché, H., Bocher, O., … Dina, C. (2022). Genetic population structure across Brittany and the downstream Loire basin provides new insights on the demographic history of Western Europe. https://doi.org/10.1101/2022.02.03.478491 https://doi.org/10.1101/2022.02.03.478491
    8. Lamothe, L., Gaignard, A., Kierkegaard, M., Hager Eldakroury, Black, M., Brancotte, B., Ison, J., Schwämmle, V., Kalaš, M., & Ménager, H. (2022). EDAM, life sciences ontology for data analysis and management. https://doi.org/10.5281/ZENODO.6769072 https://doi.org/10.5281/ZENODO.6769072
    9. Garzón, W., Benavides, L., Gaignard, A., Redon, R., & Südholt, M. (2022). A taxonomy of tools and approaches for distributed genomic analyses. Informatics in Medicine Unlocked, 32, 101024. https://doi.org/10.1016/j.imu.2022.101024 https://doi.org/10.1016/j.imu.2022.101024

    Acknowledged

    1. Canac, R., Cimarosti, B., Girardeau, A., Forest, V., Olchesqui, P., Poschmann, J., Redon, R., Lemarchand, P., Gaborit, N., & Lamirault, G. (2022). Deciphering Transcriptional Networks during Human Cardiac Development. Cells, 11(23), 3915. https://doi.org/10.3390/cells11233915 https://doi.org/10.3390/cells11233915
    2. Flippe, L., Gaignerie, A., Sérazin, C., Baron, O., Saulquin, X., Anegon, I., David, L., & Guillonneau, C. (2022). Generation of CD34\mathplusCD43\mathplus Hematopoietic Progenitors to Induce Thymocytes from Human Pluripotent Stem Cells. Cells, 11(24), 4046. https://doi.org/10.3390/cells11244046 https://doi.org/10.3390/cells11244046
    3. Canac, R., Cimarosti, B., Girardeau, A., Forest, V., Olchesqui, P., Poschmann, J., Redon, R., Lemarchand, P., Gaborit, N., & Lamirault, G. (2022). Deciphering Transcriptional Networks during Human Cardiac Development. Cells, 11(23), 3915. https://doi.org/10.3390/cells11233915 https://doi.org/10.3390/cells11233915
    4. Martinez, L., Pouvreau, J.-B., Montiel, G., Jestin, C., Delavault, P., Simier, P., & Poulin, L. (2022). Soil microbiota promotes early developmental stages of Phelipanche ramosa L. Pomel during plant parasitism on Brassica napus L. Plant and Soil, 483(1-2), 667–691. https://doi.org/10.1007/s11104-022-05822-6 https://doi.org/10.1007/s11104-022-05822-6
    5. Drouin, M., Saenz, J., Gauttier, V., Evrard, B., Teppaz, G., Pengam, S., Mary, C., Desselle, A., Thepenier, V., Wilhelm, E., Merieau, E., Ligeron, C., Girault, I., Lopez, M.-D., Fourgeux, C., Sinha, D., Baccelli, I., Moreau, A., Louvet, C., … Chiffoleau, E. (2022). CLEC-1 is a death sensor that limits antigen cross-presentation by dendritic cells and represents a target for cancer immunotherapy. Science Advances, 8(46). https://doi.org/10.1126/sciadv.abo7621 https://doi.org/10.1126/sciadv.abo7621
    6. André-Grégoire, G., Maghe, C., Douanne, T., Rosińska, S., Spinelli, F., Thys, A., Trillet, K., Jacobs, K. A., Ballu, C., Dupont, A., Lyne, A.-M., Cavalli, F. M. G., Busnelli, I., Hyenne, V., Goetz, J. G., Bidère, N., & Gavard, J. (2022). Inhibition of the pseudokinase MLKL alters extracellular vesicle release and reduces tumor growth in glioblastoma. IScience, 25(10), 105118. https://doi.org/10.1016/j.isci.2022.105118 https://doi.org/10.1016/j.isci.2022.105118
    7. Picault, S., Ezanno, P., Smith, K., Amrine, D., White, B., & Assié, S. (2022). Modelling the effects of antimicrobial metaphylaxis and pen size on bovine respiratory disease in high and low risk fattening cattle. Veterinary Research, 53(1). https://doi.org/10.1186/s13567-022-01094-1 https://doi.org/10.1186/s13567-022-01094-1
    8. Bonneaud, T. L., Lefebvre, C. C., Nocquet, L., Basseville, A., Roul, J., Weber, H., Campone, M., Juin, P. P., & Souazé, F. (2022). Targeting of MCL-1 in breast cancer-associated fibroblasts reverses their myofibroblastic phenotype and pro-invasive properties. Cell Death &Amp\Mathsemicolon Disease, 13(9). https://doi.org/10.1038/s41419-022-05214-9 https://doi.org/10.1038/s41419-022-05214-9
    9. McIlroy, D., Peltier, C., Nguyen, M.-L., Manceau, L., Mobuchon, L., Baut, N. L., Nguyen, N.-K., Tran, M.-C., Nguyen, T.-C., & Bressollette-Bodin, C. (2022). Quantification of APOBEC3 Mutation Rates Affecting the VP1 Gene of BK Polyomavirus In Vivo. Viruses, 14(9), 2077. https://doi.org/10.3390/v14092077 https://doi.org/10.3390/v14092077
    10. Ezanno, P., Picault, S., Bareille, S., Beaunée, G., Boender, G. J., Dankwa, E. A., Deslandes, F., Donnelly, C. A., Hagenaars, T. J., Hayes, S., Jori, F., Lambert, S., Mancini, M., Munoz, F., Pleydell, D. R. J., Thompson, R. N., Vergu, E., Vignes, M., & Vergne, T. (2022). The African swine fever modelling challenge: Model comparison and lessons learnt. Epidemics, 40, 100615. https://doi.org/10.1016/j.epidem.2022.100615 https://doi.org/10.1016/j.epidem.2022.100615
    11. Batta, S. P. R., Rio, M., Lebot, C., Baron-Menguy, C., Ruz, R. L., Loirand, G., & Vion, A.-C. (2022). ARHGEF18 participates in Endothelial Cell Mechano-sensitivity in Response to Flow. Acknowledged. https://doi.org/10.1101/2022.09.10.507283 https://doi.org/10.1101/2022.09.10.507283
    12. Morel, S., Hostettler, I. C., Spinner, G. R., Bourcier, R., Pera, J., Meling, T. R., Alg, V. S., Houlden, H., Bakker, M. K., van’t Hof, F., Rinkel, G. J. E., Foroud, T., Lai, D., Moomaw, C. J., Worrall, B. B., Caroff, J., Constant-dits-Beaufils, P., Karakachoff, M., Rimbert, A., … and. (2022). Intracranial Aneurysm Classifier Using Phenotypic Factors: An International Pooled Analysis. Journal of Personalized Medicine, 12(9), 1410. https://doi.org/10.3390/jpm12091410 https://doi.org/10.3390/jpm12091410
    13. Delwarde, C., Toquet, C., Aumond, P., Kayvanjoo, A. H., Foucal, A., Vely, B. L., Baudic, M., Lauzier, B., Blandin, S., Véziers, J., Paul-Gilloteaux, P., Lecointe, S., Baron, E., Massaiu, I., Poggio, P., Rémy, S., Anegon, I., Marec, H. L., Monassier, L., … Capoulade, R. (2022). Multimodality imaging and transcriptomics to phenotype mitral valve dystrophy in a unique knock-in Filamin-A rat model. Cardiovascular Research, 119(3), 759–771. https://doi.org/10.1093/cvr/cvac136 https://doi.org/10.1093/cvr/cvac136
    14. Chaumette, T., Cinotti, R., Mollé, A., Solomon, P., Castain, L., Fourgeux, C., McWilliam, H. E. G., Misme-Aucouturier, B., Broquet, A., Jacqueline, C., Vourc’h, M., Fradin, D., Bossard, C., David, L., Montassier, E., Braudeau, C., Josien, R., Villadangos, J. A., Asehnoune, K., … Roquilly, A. (2022). Monocyte Signature Associated with Herpes Simplex Virus Reactivation and Neurological Recovery after Brain Injury. American Journal of Respiratory and Critical Care Medicine, 206(3), 295–310. https://doi.org/10.1164/rccm.202110-2324oc https://doi.org/10.1164/rccm.202110-2324oc
    15. Autin, P., Deshayes, S., Lea, J., Boisgerault, N., Dupré, E., Labarrière, N., Leguevel, R., Fonteneau, J.-F., Blanquart, C., & Fradin, D. (2022). The DCMU Herbicide Shapes T-cell Functions By Modulating Micro-RNA Expression Profiles. Frontiers in Immunology, 13. https://doi.org/10.3389/fimmu.2022.925241 https://doi.org/10.3389/fimmu.2022.925241
    16. Goudal, A., Karakachoff, M., Lindenbaum, P., Baron, E., Bonnaud, S., Kyndt, F., Arnaud, M., Minois, D., Bourcereau, E., Thollet, A., Deleuze, J.-F., Genin, E., Wiart, F., Pasquié, J.-L., Galand, V., Sacher, F., Dina, C., Redon, R., Bezieau, S., … Barc, J. (2022). Burden of rare variants in arrhythmogenic cardiomyopathy with right dominant form-associated genes provides new insights for molecular diagnosis and clinical management. Human Mutation, 43(9), 1333–1342. https://doi.org/10.1002/humu.24436 https://doi.org/10.1002/humu.24436
    17. Dupas, T., Persello, A., Blangy-Letheule, A., Denis, M., Erraud, A., Aillerie, V., Leroux, A. A., Rivière, M., Lebreton, J., Tessier, A., Rozec, B., & Lauzier, B. (2022). Beneficial Effects of O-GlcNAc Stimulation in a Young Rat Model of Sepsis: Beyond Modulation of Gene Expression. International Journal of Molecular Sciences, 23(12), 6430. https://doi.org/10.3390/ijms23126430 https://doi.org/10.3390/ijms23126430
    18. Herzig, A. F., Ciullo, M., Deleuze, J.-F., Génin, E., Redon, R., Adjou, C., Chatel, S., Férec, C., Goldberg, M., Halbout, P.-A., Marec, H. L., L’Helgouach, D., Rouault, K., Schott, J.-J., Vogelsperger, A., Zins, M., Bacq, D., Blanchet, H., Boland, A., … and, H. P. (2022). Moment estimators of relatedness from low-depth whole-genome sequencing data. BMC Bioinformatics, 23(1). https://doi.org/10.1186/s12859-022-04795-8 https://doi.org/10.1186/s12859-022-04795-8
    19. Basseville, A., Violet, P.-C., Safari, M., Sourbier, C., Linehan, W. M., Robey, R. W., Levine, M., Sackett, D. L., & Bates, S. E. (2022). A Histone Deacetylase Inhibitor Induces Acetyl-CoA Depletion Leading to Lethal Metabolic Stress in RAS-Pathway Activated Cells. Cancers, 14(11), 2643. https://doi.org/10.3390/cancers14112643 https://doi.org/10.3390/cancers14112643
    20. Régimbeau, A., Budinich, M., Larhlimi, A., Karlusich, J. J. P., Aumont, O., Memery, L., Bowler, C., & Eveillard, D. (2022). Contribution of genome-scale metabolic modelling to niche theory. Ecology Letters, 25(6), 1352–1364. https://doi.org/10.1111/ele.13954 https://doi.org/10.1111/ele.13954
    21. Cimarosti, B., Canac, R., Waard, S. D., Girardeau, A., Gaignerie, A., Derevier, A., Forest, V., Ronjat, M., Marec, H. L., Gourraud, J.-B., Lemarchand, P., Waard, M. D., Lamirault, G., & Gaborit, N. (2022). Generation of human induced pluripotent stem cell lines from three patients affected by Catecholaminergic Polymorphic ventricular tachycardia (CPVT) carrying heterozygous mutations in RYR2 gene. Stem Cell Research, 60, 102688. https://doi.org/10.1016/j.scr.2022.102688 https://doi.org/10.1016/j.scr.2022.102688
    22. Tran, N. T., Lecomte, E., Saleun, S., Namkung, S., Robin, C., Weber, K., Devine, E., Blouin, V., Adjali, O., Ayuso, E., Gao, G., Penaud-Budloo, M., & Tai, P. W. L. (2022). Human and Insect Cell-Produced Recombinant Adeno-Associated Viruses Show Differences in Genome Heterogeneity. Human Gene Therapy, 33(7-8), 371–388. https://doi.org/10.1089/hum.2022.050 https://doi.org/10.1089/hum.2022.050
    23. Girardeau, A., Atticus, D., Canac, R., Cimarosti, B., Caillaud, A., Chariau, C., Simonet, F., Cariou, B., Charpentier, F., Gourraud, J.-B., Probst, V., Belbachir, N., Jesel, L., Lemarchand, P., Barc, J., Redon, R., Gaborit, N., & Lamirault, G. (2022). Generation of human induced pluripotent stem cell lines from four unrelated healthy control donors carrying European genetic background. Stem Cell Research, 59, 102647. https://doi.org/10.1016/j.scr.2021.102647 https://doi.org/10.1016/j.scr.2021.102647
    24. Küry, S., Ebstein, F., Mollé, A., Besnard, T., Lee, M.-K., Vignard, V., Hery, T., Nizon, M., Mancini, G. M. S., Giltay, J. C., Cogné, B., McWalter, K., Deb, W., Mor-Shaked, H., Li, H., Schnur, R. E., Wentzensen, I. M., Denommé-Pichon, A.-S., Fourgeux, C., … Isidor, B. (2022). Rare germline heterozygous missense variants in BRCA1-associated protein 1, BAP1, cause a syndromic neurodevelopmental disorder. The American Journal of Human Genetics, 109(2), 361–372. https://doi.org/10.1016/j.ajhg.2021.12.011 https://doi.org/10.1016/j.ajhg.2021.12.011
    25. Alberge, J.-B., Kraeber-Bodéré, F., Jamet, B., Touzeau, C., Caillon, H., Wuilleme, S., Béné, M.-C., Kampfenkel, T., Sonneveld, P., van Duin, M., Avet-Loiseau, H., Corre, J., Magrangeas, F., Carlier, T., Bodet-Milin, C., Chérel, M., Moreau, P., Minvielle, S., & Bailly, C. (2022). Molecular Signature of \lesssup\greater18\less/sup\greaterF-FDG PET Biomarkers in Newly Diagnosed Multiple Myeloma Patients: A Genome-Wide Transcriptome Analysis from the CASSIOPET Study. Journal of Nuclear Medicine, 63(7), 1008–1013. https://doi.org/10.2967/jnumed.121.262884 https://doi.org/10.2967/jnumed.121.262884
    26. Combot, Y., Salo, V. T., Chadeuf, G., Hölttä, M., Ven, K., Pulli, I., Ducheix, S., Pecqueur, C., Renoult, O., Lak, B., Li, S., Karhinen, L., Belevich, I., May, C. L., Rieusset, J., Lay, S. L., Croyal, M., Tayeb, K. S., Vihinen, H., … Prieur, X. (2022). Seipin localizes at endoplasmic-reticulum-mitochondria contact sites to control mitochondrial calcium import and metabolism in adipocytes. Cell Reports, 38(2), 110213. https://doi.org/10.1016/j.celrep.2021.110213 https://doi.org/10.1016/j.celrep.2021.110213

    2021

    Authored

    1. Meistermann, D., Bruneau, A., Loubersac, S., Reignier, A., Firmin, J., François-Campion, V., Kilens, S., Lelièvre, Y., Lammers, J., Feyeux, M., Hulin, P., Nedellec, S., Bretin, B., Castel, G., Allègre, N., Covin, S., Bihouée, A., Soumillon, M., Mikkelsen, T., … David, L. (2021). Integrated pseudotime analysis of human pre-implantation embryo single-cell transcriptomes reveals the dynamics of lineage specification. Cell Stem Cell, 28(9), 1625–1640.e6. https://doi.org/10.1016/j.stem.2021.04.027 https://doi.org/10.1016/j.stem.2021.04.027
    2. Deutschmann, I. M., Krabberød, A. K., Latorre, F., Delage, E., Marrasé, C., Balagué, V., Gasol, J. M., Massana, R., Eveillard, D., Chaffron, S., & Logares, R. (2021). Disentangling temporal associations in marine microbial networks. https://doi.org/10.1101/2021.07.13.452187 https://doi.org/10.1101/2021.07.13.452187
    3. Sayed, Z. R. A., Jouni, M., Gourraud, J.-B., Belbachir, N., Barc, J., Girardeau, A., Forest, V., Derevier, A., Gaignerie, A., Chariau, C., Cimarosti, B., Canac, R., Olchesqui, P., Charpentier, E., Schott, J.-J., Redon, R., Baró, I., Probst, V., Charpentier, F., … Gaborit, N. (2021). A consistent arrhythmogenic trait in Brugada syndrome cellular phenotype. Clinical and Translational Medicine, 11(6). https://doi.org/10.1002/ctm2.413 https://doi.org/10.1002/ctm2.413
    4. Zoppi, J., Guillaume, J.-F., Neunlist, M., & Chaffron, S. (2021). MiBiOmics: an interactive web application for multi-omics data exploration and integration. BMC Bioinformatics, 22(1). https://doi.org/10.1186/s12859-020-03921-8 https://doi.org/10.1186/s12859-020-03921-8
    5. Ison, J., Ienasescu, H., Rydza, E., Chmura, P., Rapacki, K., Gaignard, A., Schwämmle, V., van Helden, J., Kalaš, M., & Ménager, H. (2021). biotoolsSchema: a formalized schema for bioinformatics software description. GigaScience, 10(1). https://doi.org/10.1093/gigascience/giaa157 https://doi.org/10.1093/gigascience/giaa157
    6. Lefebvre, M., Gaignard, A., Folschette, M., Bourdon, J., & Guziolowski, C. (2021). Large-scale regulatory and signaling network assembly through linked open data. Database, 2021. https://doi.org/10.1093/database/baaa113 https://doi.org/10.1093/database/baaa113
    7. Charpentier, E., Cornec, M., Dumont, S., Meistermann, D., Bordron, P., David, L., Redon, R., Bonnaud, S., & Bihouée, A. (2021). 3’ RNA sequencing for robust and low-cost gene expression profiling. https://doi.org/10.21203/rs.3.pex-1336/v1 https://doi.org/10.21203/rs.3.pex-1336/v1

    Acknowledged

    1. Roudaut, M., Idriss, S., Caillaud, A., Girardeau, A., Rimbert, A., Champon, B., David, A., Lévêque, A., Arnaud, L., Pichelin, M., Prieur, X., Prat, A., Seidah, N. G., Zibara, K., May, C. L., Cariou, B., & Si-Tayeb, K. (2021). PCSK9 regulates the NODAL signaling pathway and cellular proliferation in hiPSCs. Stem Cell Reports, 16(12), 2958–2972. https://doi.org/10.1016/j.stemcr.2021.10.004 https://doi.org/10.1016/j.stemcr.2021.10.004
    2. Danger, R., Moiteaux, Q., Feseha, Y., Geffard, E., Ramstein, G., & Brouard, S. (2021). FaDA: A web application for regular laboratory data analyses. PLOS ONE, 16(12), e0261083. https://doi.org/10.1371/journal.pone.0261083 https://doi.org/10.1371/journal.pone.0261083
    3. Rose, S., Cuvellier, M., Ezan, F., Carteret, J., Bruyère, A., Legagneux, V., Nesslany, F., Baffet, G., & Langouët, S. (2021). DMSO-free highly differentiated HepaRG spheroids for chronic toxicity, liver functions and genotoxicity studies. Archives of Toxicology, 96(1), 243–258. https://doi.org/10.1007/s00204-021-03178-x https://doi.org/10.1007/s00204-021-03178-x
    4. Chaffron, S., Delage, E., Budinich, M., Vintache, D., Henry, N., Nef, C., Ardyna, M., Zayed, A. A., Junger, P. C., Galand, P. E., Lovejoy, C., Murray, A. E., Sarmento, H., Acinas, S. G., Babin, M., Iudicone, D., Jaillon, O., Karsenti, E., Wincker, P., … and, D. E. (2021). Environmental vulnerability of the global ocean epipelagic plankton community interactome. Science Advances, 7(35). https://doi.org/10.1126/sciadv.abg1921 https://doi.org/10.1126/sciadv.abg1921
    5. Gonzales, J., Marchix, J., Aymeric, L., Berre-Scoul, C. L., Zoppi, J., Bordron, P., Burel, M., Davidovic, L., Richard, J.-R., Gaman, A., Lejuste, F., Brouillet, J. Z., Vacon, F. L., Chaffron, S., Leboyer, M., Boudin, H., & Neunlist, M. (2021). Fecal Supernatant from Adult with Autism Spectrum Disorder Alters Digestive Functions, Intestinal Epithelial Barrier, and Enteric Nervous System. Microorganisms, 9(8), 1723. https://doi.org/10.3390/microorganisms9081723 https://doi.org/10.3390/microorganisms9081723
    6. Montassier, E., Valdés-Mas, R., Batard, E., Zmora, N., Dori-Bachash, M., Suez, J., & Elinav, E. (2021). Probiotics impact the antibiotic resistance gene reservoir along the human GI tract in a person-specific and antibiotic-dependent manner. Nature Microbiology, 6(8), 1043–1054. https://doi.org/10.1038/s41564-021-00920-0 https://doi.org/10.1038/s41564-021-00920-0
    7. Mutala, L. B., Deleine, C., Karakachoff, M., Dansette, D., Ducoin, K., Oger, R., Rousseau, O., Podevin, J., Duchalais, E., Fourquier, P., Thomas, W. E. A., Gourraud, P.-A., Bennouna, J., Brochier, C., Gervois, N., Bossard, C., & Jarry, A. (2021). The Caspase-1/IL-18 Axis of the Inflammasome in Tumor Cells: A Modulator of the Th1/Tc1 Response of Tumor-Infiltrating T Lymphocytes in Colorectal Cancer. Cancers, 13(2), 189. https://doi.org/10.3390/cancers13020189 https://doi.org/10.3390/cancers13020189
    8. Moreau, F., Thédrez, A., Garçon, D., Ayer, A., Sotin, T., Dijk, W., Blanchard, C., Chadeuf, G., Arnaud, L., Croyal, M., Landeghem, L. V., Touvron, M., Prieur, X., Roubtsova, A., Seidah, N., Prat, A., Cariou, B., & May, C. L. (2021). PCSK9 is not secreted from mature differentiated intestinal cells. Journal of Lipid Research, 62, 100096. https://doi.org/10.1016/j.jlr.2021.100096 https://doi.org/10.1016/j.jlr.2021.100096

    2020

    Authored

    1. Castel, G., Meistermann, D., Bretin, B., Firmin, J., Blin, J., Loubersac, S., Bruneau, A., Chevolleau, S., Kilens, S., Chariau, C., Gaignerie, A., Francheteau, Q., Kagawa, H., Charpentier, E., Flippe, L., François–Campion, V., Haider, S., Dietrich, B., Knöfler, M., … David, L. (2020). Induction of Human Trophoblast Stem Cells from Somatic Cells and Pluripotent Stem Cells. Cell Reports, 33(8), 108419. https://doi.org/10.1016/j.celrep.2020.108419 https://doi.org/10.1016/j.celrep.2020.108419
    2. Rousseau, O., Karakachoff, M., Gaignard, A., Bellanger, L., Bijlenga, P., Beaufils, P. C. D., L’Allinec, V., Levrier, O., Aguettaz, P., Desilles, J.-P., Michelozzi, C., Marnat, G., Vion, A.-C., Loirand, G., Desal, H., Redon, R., Gourraud, P.-A., & Bourcier, R. (2020). Location of intracranial aneurysms is the main factor associated with rupture in the ICAN population. Journal of Neurology, Neurosurgery &Amp\Mathsemicolon Psychiatry, 92(2), 122–128. https://doi.org/10.1136/jnnp-2020-324371 https://doi.org/10.1136/jnnp-2020-324371
    3. Nouri, A., Autrusseau, F., Bourcier, R., Gaignard, A., L’allinec, V., Menguy, C., Véziers, J., Desal, H., Loirand, G., & Redon, R. (2020). Characterization of 3D bifurcations in micro-scan and MRA-TOF images of cerebral vasculature for prediction of intra-cranial aneurysms. Computerized Medical Imaging and Graphics, 84, 101751. https://doi.org/10.1016/j.compmedimag.2020.101751 https://doi.org/10.1016/j.compmedimag.2020.101751
    4. Patin, J., Castro, C., Steenman, M., Hivonnait, A., Carcouët, A., Tessier, A., Lebreton, J., Bihouée, A., Donnart, A., Marec, H. L., Baró, I., Charpentier, F., & Derangeon, M. (2020). Gap-134, a Connexin43 activator, prevents age-related development of ventricular fibrosis in Scn5a- mice. Pharmacological Research, 159, 104922. https://doi.org/10.1016/j.phrs.2020.104922 https://doi.org/10.1016/j.phrs.2020.104922
    5. Gaignard, A., Skaf-Molli, H., & Belhajjame, K. (2020). Findable and reusable workflow data products: A genomic workflow case study. Semantic Web, 11(5), 751–763. https://doi.org/10.3233/sw-200374 https://doi.org/10.3233/sw-200374
    6. Huet, S., Pouvreau, J.-B., Delage, E., Delgrange, S., Marais, C., Bahut, M., Delavault, P., Simier, P., & Poulin, L. (2020). Populations of the Parasitic Plant Phelipanche ramosa Influence Their Seed Microbiota. Frontiers in Plant Science, 11. https://doi.org/10.3389/fpls.2020.01075 https://doi.org/10.3389/fpls.2020.01075
    7. L’Allinec, V., Chatel, S., Karakachoff, M., Bourcereau, E., Lamoureux, Z., Gaignard, A., Autrusseau, F., Jouan, S., Vion, A.-C., Loirand, G., Desal, H., Naggara, O., Redon, R., Edjlali, M., & and, R. B. (2020). Prediction of Unruptured Intracranial Aneurysm Evolution: The UCAN Project. Neurosurgery, 87(1), 150–156. https://doi.org/10.1093/neuros/nyaa093 https://doi.org/10.1093/neuros/nyaa093
    8. Chénais Benoı̂t, Cornec, M., Dumont, S., Marchand, J., & Blanckaert, V. (2020). Transcriptomic Response of Breast Cancer Cells MDA-MB-231 to Docosahexaenoic Acid: Downregulation of Lipid and Cholesterol Metabolism Genes and Upregulation of Genes of the Pro-Apoptotic ER-Stress Pathway. International Journal of Environmental Research and Public Health, 17(10), 3746. https://doi.org/10.3390/ijerph17103746 https://doi.org/10.3390/ijerph17103746
    9. Rabé, M., Dumont, S., Álvarez-Arenas, A., Janati, H., Belmonte-Beitia, J., Calvo, G. F., Thibault-Carpentier, C., Séry, Q., Chauvin, C., Joalland, N., Briand, F., Blandin, S., Scotet, E., Pecqueur, C., Clairambault, J., Oliver, L., Perez-Garcia, V., Nadaradjane, A., Cartron, P.-F., … Vallette, F. M. (2020). Identification of a transient state during the acquisition of temozolomide resistance in glioblastoma. Cell Death &Amp\Mathsemicolon Disease, 11(1). https://doi.org/10.1038/s41419-019-2200-2 https://doi.org/10.1038/s41419-019-2200-2

    Acknowledged

    1. Bakker, M. K., and Rick A. A. van der Spek, van Rheenen, W., Morel, S., Bourcier, R., Hostettler, I. C., Alg, V. S., van Eijk, K. R., Koido, M., Akiyama, M., Terao, C., Matsuda, K., Walters, R. G., Lin, K., Li, L., Millwood, I. Y., Chen, Z., Rouleau, G. A., Zhou, S., … and. (2020). Genome-wide association study of intracranial aneurysms identifies 17 risk loci and genetic overlap with clinical risk factors. Nature Genetics, 52(12), 1303–1313. https://doi.org/10.1038/s41588-020-00725-7 https://doi.org/10.1038/s41588-020-00725-7
    2. Lecomte, E., Saleun, S., Bolteau, M., Guy-Duché, A., Adjali, O., Blouin, V., Penaud-Budloo, M., & Ayuso, E. (2020). The SSV-Seq 2.0 PCR-Free Method Improves the Sequencing of Adeno-Associated Viral Vector Genomes Containing GC-Rich Regions and Homopolymers. Biotechnology Journal, 16(1). https://doi.org/10.1002/biot.202000016 https://doi.org/10.1002/biot.202000016
    3. Alberge, J.-B., Magrangeas, F., Wagner, M., Denié, S., Guérin-Charbonnel, C., Campion, L., Attal, M., Avet-Loiseau, H., Carell, T., Moreau, P., Minvielle, S., & Sérandour, A. A. (2020). DNA hydroxymethylation is associated with disease severity and persists at enhancers of oncogenic regions in multiple myeloma. Clinical Epigenetics, 12(1). https://doi.org/10.1186/s13148-020-00953-y https://doi.org/10.1186/s13148-020-00953-y
    4. Sayed, Z. R. A., Canac, R., Cimarosti, B., Bonnard, C., Gourraud, J.-B., Hamamy, H., Kayserili, H., Girardeau, A., Jouni, M., Jacob, N., Gaignerie, A., Chariau, C., David, L., Forest, V., Marionneau, C., Charpentier, F., Loussouarn, G., Lamirault, G., Reversade, B., … Gaborit, N. (2020). Human model of \lessi\greaterIRX5\less/i\greater mutations reveals key role for this transcription factor in ventricular conduction. Cardiovascular Research, 117(9), 2092–2107. https://doi.org/10.1093/cvr/cvaa259 https://doi.org/10.1093/cvr/cvaa259
    5. Roquilly, A., Jacqueline, C., Davieau, M., Mollé, A., Sadek, A., Fourgeux, C., Rooze, P., Broquet, A., Misme-Aucouturier, B., Chaumette, T., Vourc’h, M., Cinotti, R., Marec, N., Gauttier, V., McWilliam, H. E. G., Altare, F., Poschmann, J., Villadangos, J. A., & Asehnoune, K. (2020). Alveolar macrophages are epigenetically altered after inflammation, leading to long-term lung immunoparalysis. Nature Immunology, 21(6), 636–648. https://doi.org/10.1038/s41590-020-0673-x https://doi.org/10.1038/s41590-020-0673-x
    6. Seiller, C., Maiga, S., Touzeau, C., Bellanger, C., Kervoëlen, C., Descamps, G., Maillet, L., Moreau, P., Pellat-Deceunynck, C., Gomez-Bougie, P., & Amiot, M. (2020). Dual targeting of BCL2 and MCL1 rescues myeloma cells resistant to BCL2 and MCL1 inhibitors associated with the formation of BAX/BAK hetero-complexes. Cell Death &Amp\Mathsemicolon Disease, 11(5). https://doi.org/10.1038/s41419-020-2505-1 https://doi.org/10.1038/s41419-020-2505-1
    7. Frapin, M., Guignard, S., Meistermann, D., Grit, I., Moullé, V. S., Paillé, V., Parnet, P., & Amarger, V. (2020). Maternal Protein Restriction in Rats Alters the Expression of Genes Involved in Mitochondrial Metabolism and Epitranscriptomics in Fetal Hypothalamus. Nutrients, 12(5), 1464. https://doi.org/10.3390/nu12051464 https://doi.org/10.3390/nu12051464
    8. Pierre, A. S., Giemza, J., Alves, I., Karakachoff, M., Gaudin, M., Amouyel, P., Dartigues, J.-F., Tzourio, C., Monteil, M., Galan, P., Hercberg, S., Mathieson, I., Redon, R., Génin, E., & Dina, C. (2020). Correction: The genetic history of France. European Journal of Human Genetics, 28(7), 988–988. https://doi.org/10.1038/s41431-020-0604-1 https://doi.org/10.1038/s41431-020-0604-1
    9. Pham, T. H., Lecomte, S., Guevel, R. L., Lardenois, A., Evrard, B., Chalmel, F., Ferriere, F., Balaguer, P., Efstathiou, T., & Pakdel, F. (2020). Characterization of Glyceollins as Novel Aryl Hydrocarbon Receptor Ligands and Their Role in Cell Migration. International Journal of Molecular Sciences, 21(4), 1368. https://doi.org/10.3390/ijms21041368 https://doi.org/10.3390/ijms21041368
    10. Montassier, E., Al-Ghalith, G. A., Mathé, C., Bastard, Q. L., Douillard, V., Garnier, A., Guimon, R., Raimondeau, B., Touchefeu, Y., Duchalais, E., Vince, N., Limou, S., Gourraud, P.-A., Laplaud, D. A., Nicot, A. B., Soulillou, J.-P., & Berthelot, L. (2020). Distribution of Bacterial \upalpha1,3-Galactosyltransferase Genes in the Human Gut Microbiome. Frontiers in Immunology, 10. https://doi.org/10.3389/fimmu.2019.03000 https://doi.org/10.3389/fimmu.2019.03000

    2019

    Authored

    1. Belbachir, N., Portero, V., Sayed, Z. R. A., Gourraud, J.-B., Dilasser, F., Jesel, L., Guo, H., Wu, H., Gaborit, N., Guilluy, C., Girardeau, A., Bonnaud, S., Simonet, F., Karakachoff, M., Pattier, S., Scott, C., Burel, S., Marionneau, C., Chariau, C., … Scouarnec, S. L. (2019). \lessi\greaterRRAD\less/i\greater mutation causes electrical and cytoskeletal defects in cardiomyocytes derived from a familial case of Brugada syndrome. European Heart Journal, 40(37), 3081–3094. https://doi.org/10.1093/eurheartj/ehz308 https://doi.org/10.1093/eurheartj/ehz308
    2. Leveque, X., Hochane, M., Geraldo, F., Dumont, S., Gratas, C., Oliver, L., Gaignier, C., Trichet, V., Layrolle, P., Heymann, D., Herault, O., Vallette, F. M., & Olivier, C. (2019). Low-Dose Pesticide Mixture Induces Accelerated Mesenchymal Stem Cell Aging In Vitro. Stem Cells, 37(8), 1083–1094. https://doi.org/10.1002/stem.3014 https://doi.org/10.1002/stem.3014
    3. Thériault, S., Dina, C., Messika-Zeitoun, D., Scouarnec, S. L., Capoulade, R., Gaudreault, N., Rigade, S., Li, Z., Simonet, F., Lamontagne, M., Clavel, M.-A., Arsenault, B. J., Boureau, A.-S., Lecointe, S., Baron, E., Bonnaud, S., Karakachoff, M., Charpentier, E., Fellah, I., … and, J.-J. S. (2019). Genetic association analyses highlight \lessi\greaterIL6\less/i\greater, \lessi\greaterALPL\less/i\greater, and \lessi\greaterNAV1\less/i\greater as three new susceptibility genes underlying calcific aortic valve stenosis. https://doi.org/10.1101/515494 https://doi.org/10.1101/515494

    Acknowledged

    1. Bastard, Q. L., Vangay, P., Batard, E., Knights, D., & Montassier, E. (2019). US Immigration Is Associated With Rapid and Persistent Acquisition of Antibiotic Resistance Genes in the Gut. Clinical Infectious Diseases, 71(2), 419–421. https://doi.org/10.1093/cid/ciz1087 https://doi.org/10.1093/cid/ciz1087
    2. Alberge, J.-B., Magrangeas, F., Wagner, M., Denié, S., Guérin-Charbonnel, C., Campion, L., Attal, M., Avet-Loiseau, H., Carell, T., Moreau, P., Minvielle, S., & Sérandour, A. A. (2019). DNA hydroxymethylation reveals transcription regulation networks and prognostic signatures in multiple myeloma. Acknowledged. https://doi.org/10.1101/806133 https://doi.org/10.1101/806133
    3. Leroy, T., Louvet, J.-M., Lalanne, C., Provost, G. L., Labadie, K., Aury, J.-M., Delzon, S., Plomion, C., & Kremer, A. (2019). Adaptive introgression as a driver of local adaptation to climate in European white oaks. New Phytologist, 226(4), 1171–1182. https://doi.org/10.1111/nph.16095 https://doi.org/10.1111/nph.16095
    4. Leroy, T., Rougemont, Q., Dupouey, J.-L., Bodénès, C., Lalanne, C., Belser, C., Labadie, K., Provost, G. L., Aury, J.-M., Kremer, A., & Plomion, C. (2019). Massive postglacial gene flow between European white oaks uncovered genes underlying species barriers. New Phytologist, 226(4), 1183–1197. https://doi.org/10.1111/nph.16039 https://doi.org/10.1111/nph.16039
    5. Guimbretiere, G., Scouarnec, S. L., Rigade, S., Boureau, A. S., Cueff, C., Capoulade, R., Dina, C., Mérot, J., Schott, J. J., & Tourneau, T. L. (2019). Phenotypic and genotypic approach of a large family with early onset tricuspid aortic valve sclerosis-stenosis: A multimodality evaluation. Archives of Cardiovascular Diseases Supplements, 11(1), 66–67. https://doi.org/10.1016/j.acvdsp.2018.10.145 https://doi.org/10.1016/j.acvdsp.2018.10.145

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