2023

Ngoc-Khanh Nguyen, Marie-Claire Devilder, Laetitia Gautreau-Rolland, Cynthia Fourgeux, Debajyoti Sinha, Jeremie Poschmann, Maryvonne Hourmant, Céline Bressollette-Bodin, Xavier Saulquin, Dorian McIlroy
B-cell repertoire against BKPyV
Life Science Alliance Jan 2023, 6 (4) e202201567. doi:10.26508/lsa.202201567
2022

Lucie Lamothe, Alban Gaignard, Mads Kierkegaard, Hager Eldakroury, Melissa Black, Bryan Brancotte, Jon Ison, Veit Schwämmle, Matúš Kalaš, Hervé Ménager
EDAM, the life-science ontology for data analysis and management
Zenodo. doi: 10.5281/zenodo.6769072

Guillermo Dominguez-Huerta, Ahmed Zayed, James Wainaina, Jiarong Guo, Funing Tian, Akbar Adjie Pratama, Benjamin Bolduc, Mohamed Mohssen, Olivier Zablocki, Eric Pelletier, Erwan Delage, Adriana Alberti, Jean-Marc Aury, Quentin Carradec, Corinne da Silva, Karine Labadie, Julie Poulain, Chris Bowler, Damien Eveillard, Lionel Guidi, Eric Karsenti, Jens Kuhn, Hiroyuki Ogata, Patrick Wincker, Alexander Culley, Samuel Chaffron, Matthew Sullivan
Diversity and ecological footprint of Global Ocean RNA viruses
Science. 2022 Jun 10;376(6598):1202-1208. doi: 10.1126/science.abn6358

Ahmed Zayed, James Wainaina, Guillermo Dominguez-Huerta, Eric Pelletier, Jiarong Guo, Mohamed Mohssen, Funing Tian, Akbar Adjie Pratama, Benjamin Bolduc, Olivier Zablocki, Dylan Cronin, Lindsey Solden, Erwan Delage, Adriana Alberti, Jean-Marc Aury, Quentin Carradec, Corinne da Silva, Karine Labadie, Julie Poulain, Hans-Joachim Ruscheweyh, Guillem Salazar, Elan Shatoff, Ralf Bundschuh, Kurt Fredrick, Laura Kubatko, Samuel Chaffron, Alexander Culley, Shinichi Sunagawa, Jens Kuhn, Patrick Wincker, Matthew Sullivan, Silvia Acinas, Marcel Babin, Peer Bork, Emmanuel Boss, Chris Bowler, Guy Cochrane, Colomban de Vargas, Gabriel Gorsky, Lionel Guidi, Nigel Grimsley, Pascal Hingamp, Daniele Iudicone, Olivier Jaillon, Stefanie Kandels, Lee Karp-Boss, Eric Karsenti, Fabrice Not, Hiroyuki Ogata, Nicole Poulton, Stéphane Pesant, Christian Sardet, Sabrinia Speich, Lars Stemmann, Matthew Sullivan, Shinichi Sungawa, Patrick Wincker
Cryptic and abundant marine viruses at the evolutionary origins of Earth’s RNA virome
Science. 2022 Apr 8;376(6589):156-162.  doi: 10.1126/science.abm5847

Barbara Misme‐aucouturier, Marion de Carvalho, Erwan Delage, Eléonore Dijoux, Martin Klein, Carole Brosseau, Marie Bodinier, Laurence Guzylack-Piriou, G. Bouchaud
Oral exposure to bisphenol A exacerbates allergic inflammation in a mouse model of food allergy
Toxicology. 2022 Apr 30;472:153188. doi: 10.1016/j.tox.2022.153188

Ina Maria Deutschmann, Anders Krabberød, Francisco Latorre, Erwan Delage, Cèlia Marrasé, Vanessa Balagué, Josep Gasol, Ramon Massana, Damien Eveillard, Samuel Chaffron, Ramiro Logares
Disentangling temporal associations in marine microbial networks
bioRxiv.  doi: 10.1101/2021.07.13.452187


Thomas L Bonneaud, Chloé Lefebvre, Lisa Nocquet, Agnes Basseville, Julie Roul, Hugo Weber, Mario Campone, Philippe P Juin, Frédérique Souazé
Targeting of MCL-1 in breast cancer-associated fibroblasts reverses their myofibroblastic phenotype and pro-invasive properties
Cell Death Dis 13, 787 (2022). doi: 10.1038/s41419-022-05214-9

Jean-Baptiste Alberge, Françoise Kraeber-Bodéré, Bastien Jamet, Cyrille Touzeau, Hélène Caillon, Soraya Wuilleme, Marie-Christine Béné, Tobias Kampfenkel, Pieter Sonneveld, Mark van Duin, Herve Avet-Loiseau, Jill Corre, Florence Magrangeas, Thomas Carlier, Caroline Bodet-Milin, Michel Chérel, Philippe Moreau, Stéphane Minvielle, Clément Bailly
Molecular Signature of 18 F-FDG PET Biomarkers in Newly Diagnosed Multiple Myeloma Patients: A Genome-Wide Transcriptome Analysis from the CASSIOPET Study
J Nucl Med. 2022 Jul;63(7):1008-1013. doi: 10.2967/jnumed.121.262884

Salomé Decombis, Antonin Papin, Céline Bellanger, Clara Sortais, Christelle Dousset, Yannick Le Bris, Thiphanie Riveron, Stéphanie Blandin, Philippe Hulin, Benoit Tessoulin, Mathieu Rouel, Steven Le Gouill, Agnès Moreau-Aubry, Catherine Pellat-Deceunynck, David Chiron
The IL32/BAFF axis supports prosurvival dialogs in the lymphoma ecosystem and is disrupted by NIK inhibition
Haematologica. 2022 Dec 1;107(12):2905-2917. doi: 10.3324/haematol.2021.279800.

Dupas, T., Persello, A., Blangy-Letheule, A., Denis, M., Erraud, A., Aillerie, V., ... & Lauzier, B.
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

Canac R, Cimarosti B, Girardeau A, Forest V, Olchesqui P, Poschmann J, Redon R, Lemarchand P, Gaborit N, Lamirault G.
Deciphering transcriptional networks during human cardiac development.
Cells, 11(23), 3915. https://doi.org/10.3390/cells11233915
 
Flippe, L., Gaignerie, A., Sérazin, C., Baron, O., Saulquin, X., Anegon, I., ... & Guillonneau, C.
Generation of CD34+ CD43+ hematopoietic progenitors to induce thymocytes from human pluripotent stem cells.
Cells, 11(24), 4046. https://doi.org/10.3390/cells11244046
 
Batta, S. P. R., Rio, M., Lebot, C., Baron-Menguy, C., Le Ruz, R., Loirand, G., & Vion, A. C.
ARHGEF18 participates in Endothelial Cell Mechano-sensitivity in Response to Flow.
bioRxiv. https://doi.org/10.1101/2022.09.10.507283
 
Basseville, A., Violet, P. C., Safari, M., Sourbier, C., Linehan, W. M., Robey, R. W., ... & Bates, S. E.
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
 
Autin, P., Deshayes, S., Lea, J., Boisgerault, N., Dupré, E., Labarrière, N., ... & Fradin, D. 
The DCMU herbicide shapes T cell functions by modulating micro-RNA expression profiles.
Frontiers in Immunology, 3736. https://doi.org/10.3389/fimmu.2022.925241
 
Robin Canac, Bastien Cimarosti, Aurore Girardeau, Virginie Forest, Pierre Olchesqui, Jeremie Poschmann, Richard Redon, Patricia Lemarchand, Nathalie Gaborit, Guillaume Lamirault 
Deciphering Transcriptional Networks during Human Cardiac Development
Cells. 2022 Dec 3;11(23):3915. doi: 10.3390/cells11233915

Xavier Vanhoye, Claire Bardel, Antoine Rimbert, Philippe Moulin, Pierre-Antoine Rollat-Farnier, Manon Muntaner, Oriane Marmontel, Sabrina Dumont, Sybil Charrière, François Cornélis, Pierre Henri Ducluzeau, Annie Fonteille, Estelle Nobecourt, Noël Peretti, Franck Schillo, Matthieu Wargny, Bertrand Cariou, Aline Meirhaeghe, Mathilde Di Filippo,
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, 2022, ISSN 1931-5244. doi : 10.1016/j.trsl.2022.12.002.

Francine Jotereau, Joudy Alameddine, Raluca Teusan, Annabelle Pedron, Nicolas Jouand, Frederic Altare and Emmanuelle Godefroy
Human gut microbiota-reactive DP8a regulatory T cells, signature and related emerging functions
Frontiers in Immunology, 2022, 13, doi:10.3389/fimmu.2022.1026994

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 MD,  FOURGEUX C, SINHA D, BACCELLI I, MOREAU A, LOUVET C, JOSIEN R, POSCHMANN J, POIRIER N AND CHIFFOLEAU E
CLEC-1 is a death sensor that limits antigen cross-presentation by dendritic cells and represents a target for cancer immunotherapy
SCIENCE ADVANCES, 18 Nov 2022, Vol 8, Issue 46, doi:10.1126/sciadv.abo7621

Gwennan Andre-Gregoire, Clement Maghe, Tiphaine Douanne, Sara Rosinska, Fiorella Spinelli, An Thys, Kilian Trillet, Kathryn A. Jacobs, Cyndie Ballu,Aurelien Dupont, Anne-Marie Lyne, Florence M.G. Cavalli, Ignacio Busnelli, Vincent Hyenne, Jacky G. Goetz, Nicolas Bidere, and Julie Gavard 
Inhibition of the pseudokinase MLKL alters extracellular vesicle release and reduces tumor growth in glioblastoma
iScience 25, 105118, October 21, 2022, doi:10.1016/j.isci. 2022.105118

Sébastien Picault, Pauline Ezanno, Kristen Smith, David Amrine, Brad White & Sébastien Assié 
Modelling the effects of antimicrobial metaphylaxis and pen size on bovine respiratory disease in high and low risk fattening cattle
Veterinary Research volume 53, Article number: 77 (2022) doi10.1186/s13567-022-01094-1

Dorian McIlroy, Cécile Peltier, My-Linh Nguyen, Louise Manceau, Lenha Mobuchon, Nicolas Le Baut, Ngoc-Khanh Nguyen, Minh-Chau Tran, The-Cuong Nguyen and Céline Bressollette-Bodin
Quantification of APOBEC3 Mutation Rates Affecting the VP1 Gene of BK Polyomavirus In Vivo
Viruses 2022, 14(9), 2077; doi: 10.3390/v14092077

Sandrine Morel, Isabel C. Hostettler, Georg R. Spinner, Romain Bourcier, Joanna Pera, Torstein R. Meling, Varinder S. Alg, Henry Houlden, Mark K. Bakker , Femke van’t Hof, Gabriel J. E. Rinkel, Tatiana Foroud, Dongbing Lai, Charles J. Moomaw, Bradford B. Worrall, Jildaz Caroff, Pacôme Constant-dits-Beaufils, Matilde Karakachoff, Antoine Rimbert, Aymeric Rouchaud, Emilia I. Gaal-Paavola, Hanna Kaukovalta, Riku Kivisaari, Aki Laakso, Behnam Rezai Jahromi , Riikka Tulamo, Christoph M. Friedrich, Jerome Dauvillier, Sven Hirsch , Nathalie Isidor, Zolt Kulcsàr, Karl O. Lövblad, Olivier Martin, Paolo Machi, Vitor Mendes Pereira, Daniel Rüfenacht, Karl Schaller, Sabine Schilling , Agnieszka Slowik, Juha E. Jaaskelainen, Mikael von und zu Fraunberg, Jordi Jiménez-Conde, Elisa Cuadrado-Godia, Carolina Soriano-Tárraga, Iona Y. Millwood, Robin G. Walters, The @neurIST project, The ICAN Study Group, Genetics and Observational Subarachnoid Haemorrhage (GOSH) Study Investigators, International Stroke Genetics Consortium (ISGC), Helen Kim, Richard Redon, Nerissa U. Ko, Guy A. Rouleau, Antti Lindgren, Mika Niemelä, Hubert Desal, Daniel Woo, Joseph P. Broderick, David J.Werring, Ynte M. Ruigrok and Philippe Bijlenga 
Intracranial Aneurysm Classifier Using Phenotypic Factors: An International Pooled Analysis
J. Pers. Med. 2022, 12(9), 1410; doi: 10.3390/jpm12091410

C Delwarde, C Toquet, P Aumond, A Hossein Kayvanjoo, A Foucal, B Le Vely, M Baudic, B Lauzier, S Blandin, J Véziers, P Paul-Gilloteaux, S Lecointe, E Baron, I Massaiu, P Poggio, S Rémy, I Anegon, H Le Marec, L Monassier, JJ Schott, E Mass, J Barc, T Le Tourneau, J Merot, R Capoulade
Multimodality imaging and transciptomics to phenotype mitral valve dystrophy in a unique knock-in Filamin-A rat model.
Cardiovascular Research, 2022 Aug 24 cvac136, doi: 10.1093/cvr/cvac136

Régimbeau A, Budinich M, Larhlimi A, Pierella Karlusich JJ, Aumont O, Memery L, Bowler C, Eveillard D.
Contribution of genome-scale metabolic modelling to niche theory.
Ecol Lett. 2022 Jun;25(6):1352-1364. doi: 10.1111/ele.13954.

Churcheward B, Millet M, Bihouée A, Fertin G, Chaffron S.
MAGNETO: An Automated Workflow for Genome-Resolved Metagenomics.
mSystems. 2022 Jun 15:e0043222. doi: 10.1128/msystems.00432-22. PMID: 35703559.

Chaumette T, Cinotti R, Mollé A, Solomon P, Castain L, Fourgeux C, McWilliam HEG, Misme-Aucouturier B, Broquet A, Jacqueline C, Vourc'h M, Fradin D, Bossard C, David L, Montassier E, Braudeau C, Josien R, Villadangos JA, Asehnoune K, Bressollette-Bodin C, Poschmann J, Roquilly A.
Monocyte Signature Associated with Herpes Simplex Virus Reactivation and Neurological Recovery after Brain Injury.
Am J Respir Crit Care Med. 2022 Aug 1;206(3):295-310. PMID: 35486851. doi: 10.1164/rccm.202110-2324OC.

Pauline Ezanno, Sébastien Picault, Servane Bareille, Gaël Beaunée, Gert Jan Boender, Emmanuelle A. Dankwa, François Deslandes, Christl A. Donnelly, Thomas J. Hagenaars, Sarah Hayes, Ferran Jori, Sébastien Lambert, Matthieu Mancini, Facundo Munoz, David R.J. Pleydell, Robin N. Thompson, Elisabeta Vergu, Matthieu Vignes, Timothée Vergne.
The African swine fever modelling challenge: Model comparison and lessons learnt.
Epidemics,Volume 40,2022,100615,ISSN 1755-4365. doi: 10.1016/j.epidem.2022.100615

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, 13331342. doi: 10.1002/humu.24436

Herzig, A.F., Ciullo, M., FranceGenRef Consortium. et al.
Moment estimators of relatedness from low-depth whole-genome sequencing data.
BMC Bioinformatics 23, 254 (2022). doi: 10.1186/s12859-022-04795-8

Bastien Cimarosti, Robin Canac, Stephan De Waard, Aurore Girardeau, Anne Gaignerie, Aude Derevier, Virginie Forest, Michel Ronjat, Hervé Le Marec, Jean-Baptiste Gourraud, Patricia Lemarchand, Michel De Waard, Guillaume Lamirault, Nathalie Gaborit.
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,Volume 60,2022,102688,ISSN 1873-5061. doi: 10.1016/j.scr.2022.102688.

Ngoc Tam Tran, Emilie Lecomte, Sylvie Saleun, Suk Namkung, Cecile Robin, Kristina Weber, Eric Devine, Veronique Blouin, Oumeya ADJALI, Eduard Ayuso, Guangping Gao, Magalie Penaud-Budloo, and Phillip W.L. Tai
Human and insect cell-produced rAAVs show differences in genome heterogeneity
Human Gene Therapy, Mar 2022 doi: 10.1089/hum.2022.050

Barc J, Tadros R, Glinge C, Chiang DY, Jouni M, Simonet F, Jurgens SJ, Baudic M, Nicastro M, Potet F, Offerhaus JA, Walsh R, Choi SH, Verkerk AO, Mizusawa Y, Anys S, Minois D, Arnaud M, Duchateau J, Wijeyeratne YD, Muir A, Papadakis M, Castelletti S, Torchio M, Ortuño CG, Lacunza J, Giachino DF, Cerrato N, Martins RP, Campuzano O, Van Dooren S, Thollet A, Kyndt F, Mazzanti A, Clémenty N, Bisson A, Corveleyn A, Stallmeyer B, Dittmann S, Saenen J, Noël A, Honarbakhsh S, Rudic B, Marzak H, Rowe MK, Federspiel C, Le Page S, Placide L, Milhem A, Barajas-Martinez H, Beckmann BM, Krapels IP, Steinfurt J, Winkel BG, Jabbari R, Shoemaker MB, Boukens BJ, Škorić-Milosavljević D, Bikker H, Manevy FC, Lichtner P, Ribasés M, Meitinger T, Müller-Nurasyid M; KORA-Study Group, Veldink JH, van den Berg LH, Van Damme P, Cusi D, Lanzani C, Rigade S, Charpentier E, Baron E, Bonnaud S, Lecointe S, Donnart A, Le Marec H, Chatel S, Karakachoff M, Bézieau S, London B, Tfelt-Hansen J, Roden D, Odening KE, Cerrone M, Chinitz LA, Volders PG, van de Berg MP, Laurent G, Faivre L, Antzelevitch C, Kääb S, Arnaout AA, Dupuis JM, Pasquie JL, Billon O, Roberts JD, Jesel L, Borggrefe M, Lambiase PD, Mansourati J, Loeys B, Leenhardt A, Guicheney P, Maury P, Schulze-Bahr E, Robyns T, Breckpot J, Babuty D, Priori SG, Napolitano C; Nantes Referral Center for inherited cardiac arrhythmia, de Asmundis C, Brugada P, Brugada R, Arbelo E, Brugada J, Mabo P, Behar N, Giustetto C, Molina MS, Gimeno JR, Hasdemir C, Schwartz PJ, Crotti L, McKeown PP, Sharma S, Behr ER, Haissaguerre M, Sacher F, Rooryck C, Tan HL, Remme CA, Postema PG, Delmar M, Ellinor PT, Lubitz SA, Gourraud JB, Tanck MW, George AL Jr, MacRae CA, Burridge PW, Dina C, Probst V, Wilde AA, Schott JJ, Redon R, Bezzina CR.
Genome-wide association analyses identify new Brugada syndrome risk loci and highlight a new mechanism of sodium channel regulation in disease susceptibility.
Nat Genet. 2022 Feb 24. doi: 10.1038/s41588-021-01007-6

Isabel Alves, Joanna Giemza, Michael Blum, Carolina Bernhardsson, Stéphanie Chatel, Matilde Karakachoff, Aude Saint Pierre, Anthony F. Herzig, Robert Olaso, Martial Monteil, Véronique Gallien, Elodie Cabot, Emma Svensson, Delphine Bacq-Daian, Estelle Baron, Charlotte Berthellier, Céline Besse, Hélène Blanché, Ozvan Bocher, Anne Boland, Stéphanie Bonnaud, Eric Charpentier, Claire Dandine-Roulland, Claude Férec, Christine Fruchet, Simon Lecointe, Edith Le Floch, Thomas Ludwig, Gaëlle Marenne, Vincent Meyer, Elisabeth Quellery, Fernando Racimo, Karen Rouault, Florian Sandron, Jean-Jacques Schott, Lourdes Velo Suarez, Jade Violleau, Eske Willerslev, Yves Coativy, Mael Jézéquel, Daniel Le-Bris, Clément Nicolas, Yvan Pailler, Marcel Goldberg, Marie Zins, Hervé Le-Marec, Mattias Jakobsson, Pierre Darlu, Emmanuelle Génin, Jean-François Deleuze, Richard Redon, Christian Dina
Genetic population structure across Brittany and the downstream Loire basin provides new insights on the demographic history of Western Europe
bioRxiv 2022.02.03.478491; doi: 10.1101/2022.02.03.478491

Kury S, Ebstein F, Mollé A, Besnard T, Lee, M-K, Vignard V, Hery T, Nizon M, Mancini G, Giltay J, Cogné B, McWalter K, Deb W, Mor-Shaked H, Li H, Schnur R, Wentzensen I, Denommé-Pichon AS, Isidor B
Rare germline heterozygous missense variants in BRCA1-associated protein 1, BAP1, cause a syndromic neurodevelopmental disorder
AJHG, january 2022 https://doi.org/10.1016/j.ajhg.2021.12.011

Yoann Combot, Veijo T. Salo, Gilliane Chadeuf, Maarit Hölttä, Katharina Ven, Ilari Pulli, Simon Ducheix, Claire Pecqueur, Ophélie Renoult, Behnam Lak, Shiqian Li, Leena Karhinen, Ilya Belevich, Cedric Le May, Jennifer Rieusset, Soazig Le Lay, Mikael Croyal, Karim Si Tayeb, Helena Vihinen, Eija Jokitalo, Kid Törnquist, Corinne Vigouroux, Bertrand Cariou, Jocelyne Magré, Abdelhalim Larhlimi, Elina Ikonen, Xavier Prieur.
Seipin localizes at endoplasmic-reticulum-mitochondria contact sites to control mitochondrial calcium import and metabolism in adipocytes.
Cell Reports,Volume 38, Issue 2, 2022. doi: https://doi.org/10.1016/j.celrep.2021.110213
2021

Aurore Girardeau, Diane Atticus, Robin Canac, Bastien Cimarosti, Amandine Caillaud, Caroline Chariau, Floriane Simonet, Bertrand Cariou, Flavien Charpentier, Jean-Baptiste Gourraud, Vincent Probst, Nadjet Belbachir, Laurence Jesel, Patricia Lemarchand, Julien Barc, Richard Redon, Nathalie Gaborit, Guillaume Lamirault.
Generation of human induced pluripotent stem cell lines from four unrelated healthy control donors carrying European genetic background,
Stem Cell Research 2021. doi: https://doi.org/10.1016/j.scr.2021.102647

Richard Danger, Quentin Moiteaux, Yodit Feseha, Estelle Geffard, Gérard Ramstein, Sophie Brouard.
FaDA: A web application for regular laboratory data analyses
PLOS ONE, December 20, 2021. doi: https://doi.org/10.1371/journal.pone.0261083

Rose, S., Cuvellier, M., Ezan, F. et al. 
DMSO-free highly differentiated HepaRG spheroids for chronic toxicity, liver functions and genotoxicity studies. 
Arch Toxicol, 2021. doi: https://doi.org/10.1007/s00204-021-03178-x

Meryl Roudaut, Salam Idriss, Amandine Caillaud, Aurore Girardeau, Antoine Rimbert, Benoite Champon, Amandine David, Antoine Lévêque, Lucie Arnaud, Matthieu Pichelin, Xavier Prieur, Annik Prat, Nabil G. Seidah, Kazem Zibara, Cedric Le May, Bertrand Cariou, Karim Si-Tayeb
PCSK9 regulates the NODAL signaling pathway and cellular proliferation in hiPSCs.
Stem Cell Reports,2021,ISSN 2213-6711, doi:10.1016/j.stemcr.2021.10.004

Al Sayed ZR, Jouni M, Gourraud JB, Belbachir N, Barc J, Girardeau A, Forest V, Derevier A, Gaignerie A, Chariau C, Cimarosti B, Canac R, Olchesqui P, Charpentier E, Schott JJ, Redon R, Baró I, Probst V, Charpentier F, Loussouarn G, Zibara K, Lamirault G, Lemarchand P, Gaborit N.
A consistent arrhythmogenic trait in Brugada syndrome cellular phenotype.
Clin Transl Med. 2021 Jun;11(6):e413. doi: 10.1002/ctm2.413

Chaffron S, Delage E, Budinich M, Vintache D, Henry N, Nef C, Ardyna M, Zayed AA, Junger PC, Galand PE, Lovejoy C, Murray AE, Sarmento H; Tara Oceans coordinators, Acinas SG, Babin M, Iudicone D, Jaillon O, Karsenti E, Wincker P, Karp-Boss L, Sullivan MB, Bowler C, de Vargas C, Eveillard D.
Environmental vulnerability of the global ocean epipelagic plankton community interactome.
Sci Adv. 2021 Aug 27;7(35):eabg1921. doi: 10.1126/sciadv.abg1921

Alban Gaignard, Hala Skaf-Molli, Khalid Belhajjame
Découvrabilité et réutilisation de données produites par des workflows: un cas d'usage en génomique
PFIA 2021, HAL Id: emse-03261182

Zeina R Al Sayed, Robin Canac, Bastien Cimarosti, Carine Bonnard, Jean-Baptiste Gourraud, Hanan Hamamy, Hulya Kayserili, Aurore Girardeau, Mariam Jouni, Nicolas Jacob
Human model of IRX5 mutations reveals key role for this transcription factor in ventricular conduction
Cardiovascular Research, Volume 117, Issue 9, August 2021, doi:10.1093/cvr/cvaa259

Montassier, E., Valdés-Mas, R., Batard, E. et al.
Probiotics impact the antibiotic resistance gene reservoir along the human GI tract in a person-specific and antibiotic-dependent manner.
Nat Microbiol 6, 1043–1054 (2021), doi:10.1038/s41564-021-00920-0

Eric Charpentier, Marine Cornec, Solenne Dumont et al. 3’ RNA sequencing for robust and low-cost gene expression profiling, 28 January 2021, PREPRINT (Version 1) available at Research Square [https://doi.org/10.21203/rs.3.pex-1336/v1]Eric Charpentier, Marine Cornec, Solenne Dumont et al. 3’ RNA sequencing for robust and low-cost gene expression profiling, 28 January 2021, PREPRINT (Version 1) available at Research Square [https://doi.org/10.21203/rs.3.pex-1336/v1]Eric Charpentier, Marine Cornec, Solenne Dumont et al. 3’ RNA sequencing for robust and low-cost gene expression profiling, 28 January 2021, PREPRINT (Version 1) available at Research Square [https://doi.org/10.21203/rs.3.pex-1336/v1]Moreau F, Thédrez A, Garçon D, Ayer A, Sotin T, Dijk W, Blanchard C, Chadeuf G, Arnaud L, Croyal M, Van Landeghem L, Touvron M, Prieur X, Roubtsova A, Seidah N, Prat A, Cariou B, Le May C
PCSK9 is not secreted from mature differentiated intestinal cells
Journal of Lipid Research, July 2021, doi:10.1016/j.jlr.2021.100096

Gonzales J, Marchix J, Aymeric L, Le Berre-Scoul C, Zoppi J, Bordron P, Burel M, Davidovic L, Richard J-R, Gaman A, Lejuste F, Brouillet J, Le Vacon F, Chaffron S, Leboyer M, Boudin H and Neunlist M
Fecal Supernatant from Adult with Autism Spectrum Disorder Alters Digestive Functions, Intestinal Epithelial Barrier, and Enteric Nervous System
Microorganisms 2021, 9, 1723. doi:10.3390/microorganisms9081723

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, Barrière P, Chazaud C, Chappell J, Pasque V, Bourdon J, Fréour T, David L.
Integrated pseudotime analysis of human pre-implantation embryo single-cell transcriptomes reveals the dynamics of lineage specification.
Cell Stem Cell. 2021 May 10:S1934-5909(21)00185-5. doi: 10.1016/j.stem.2021.04.027

Ison J, Ienasescu H, Rydza E, Chmura P, Rapacki K, Gaignard A, Schwämmle V, van Helden J, Kalaš M, Ménager H.
biotoolsSchema: a formalized schema for bioinformatics software description.
Gigascience. 2021 Jan 27;10(1):giaa157. doi: 10.1093/gigascience/giaa157

Eric Charpentier, Marine Cornec, Solenne Dumont, Dimitri Meistermann, Philippe Bordron, Laurent David, Richard Redon, Stéphanie Bonnaud, Audrey Bihouée
3’ RNA sequencing for robust and low-cost gene expression profiling.
Research Square, 28 January 2021, doi: 10.21203/rs.3.pex-1336/v1

M Lefebvre, A Gaignard, M Folschette, J Bourdon, C Guziolowski.
Large-scale regulatory and signaling network assembly through linked open data.
Database, Volume 2021, 2021, baaa113, doi: 10.1093/database/baaa113

Mutala LB, Deleine C, Karakachoff M, Dansette D, Ducoin K, Oger R, Rousseau O, Podevin J, Duchalais E, Fourquier P, Thomas WEA, Gourraud PA, Bennouna J, Brochier C, Gervois N, Bossard C, Jarry A.
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 (Basel). 2021 Jan 7;13(2):E189. doi: 10.3390/cancers13020189.

Johanna Zoppi, Jean-François Guillaume, Michel Neunlist, Samuel Chaffron
MiBiOmics: An interactive web application for multi-omics data exploration and integration
BMC Bioinformatics 22, 6 (2021)  doi: 10.1186/s12859-020-03921-8

2020

Bakker M et al.Bakker, M.K., van der Spek, R.A.A., van Rheenen, W. et al.
Genome-wide association study of intracranial aneurysms identifies 17 risk loci and genetic overlap with clinical risk factors.
Nat Genet 52, 1303–1313 (2020). doi: 10.1038/s41588-020-00725-7

A. Nouri, F. Autrusseau, R. Bourcier, A. Gaignard, V. L’allinec, C. Menguy, J. Véziers, H. Desal, G. Loirand, R. Redon,
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, Volume 84, 2020,101751,ISSN 0895-6111 . doi: 10.1016/j.compmedimag.2020.101751

Rousseau O, Karakachoff M, Gaignard A, Bellanger L, Bijlenga P, Constant Dit Beaufils P, L'Allinec V, Levrier O, Aguettaz P, Desilles JP, Michelozzi C, Marnat G, Vion AC, Loirand G, Desal H, Redon R, Gourraud PA, Bourcier R; ICAN Investigators.
Location of intracranial aneurysms is the main factor associated with rupture in the ICAN population.
J Neurol Neurosurg Psychiatry. 2020 Oct 23:jnnp-2020-324371. doi: 10.1136/jnnp-2020-324371.

Lecomte E, Saleun S, Bolteau M, Guy-Duché A, Adjali O, Blouin V, Penaud-Budloo M, Ayuso E.
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 (2020) ISSN: 1860-6768 Online ISSN: 1860-7314. doi: 10.1002/biot.202000016

Gaël Castel, Dimitri Meistermann, Betty Bretin, Julie Firmin, Justine Blin, Sophie Loubersac, Alexandre Bruneau, Simon Chevolleau, Stéphanie Kilens, Caroline Chariau, Anne Gaignerie, Quentin Francheteau, Harunobu Kagawa, Eric Charpentier, Léa Flippe, Valentin François--Campion, Sandra Haider, Bianca Dietrich, Martin Knöfler, Takahiro Arima, Jérémie Bourdon, Nicolas Rivron, Damien Masson, Thierry Fournier, Hiroaki Okae, Thomas Fréour, Laurent David.
Induction of Human Trophoblast Stem Cells from Somatic Cells and Pluripotent Stem Cells,
Cell Reports,Volume 33, Issue 8,2020,108419,ISSN 2211-1247. doi: 10.1016/j.celrep.2020.108419

Jean-Baptiste Alberge, Florence Magrangeas, Mirko Wagner, Soline Denié, Catherine Guérin-Charbonnel, Loïc Campion, Michel Attal, Hervé Avet-Loiseau, Thomas Carell, Philippe Moreau, Stéphane Minvielle, Aurélien A. Sérandour
DNA hydroxymethylation reveals transcription regulation networks and prognostic signatures in multiple myeloma
Clin Epigenet 12, 163 (2020). doi: 10.1186/s13148-020-00953-y

Alban Gaignard, Hala Skaf-Molli, Khalid Belhajjame
Findable and reusable workflow data products: A genomic workflow case study
Semantic Web Journal, IOS Press, 2020, pp.1-13. doi:10.3233/SW-200374

Vincent l'Allinec, Stéphanie Chatel, Matilde Karakachoff, Emmanuelle Bourcereau, Zeineb Es-Salah-Lamoureux, Alban Gaignard et al.
Prediction of Unruptured Intracranial Aneurysm Evolution: The UCAN Project
Neurosurgery, 2020 July 1;87(1):150-156. doi:10.1093/neuros/nyaa093

Huet S, Pouvreau J-B, Delage E, Delgrange S, Marais C, Bahut M, Delavault P, Simier P and Poulin L
Populations of the Parasitic Plant Phelipanche ramosa Influence Their Seed Microbiota
Front. Plant Sci., 17 July 2020. doi: 10.3389/fpls.2020.01075

Patin J, Castro C, Steenman M, Hivonnait A, Carcouët A, Tessier A, Lebreton J, Bihouée A, Donnart A, Le Marec H, Baró I, Charpentier F, Derangeon M.
Gap-134, a Connexin43 activator, prevents age-related development of ventricular fibrosis in Scn5a+/- mice.
Pharmacol Res 2020;104922. doi:10.1016/j.phrs.2020.104922

Chénais B, Cornec M, Dumont S, Marchand J, Blanckaert V
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
Int J Environ Res Public Health 2020;17. doi: 10.3390/ijerph17103746

Antoine Roquilly, Cedric Jacqueline, Marion Davieau, Alice Mollé, Abderrahmane Sadek, Cynthia Fourgeux, Paul Rooze, Alexis Broquet, Barbara Misme-Aucouturier, Tanguy Chaumette, Mickael Vourc'h, Raphael Cinotti, Nadege Marec, Vanessa Gauttier, Hamish E G McWilliam, Frederic Altare, Jeremie Poschmann, Jose A Villadangos, Karim Asehnoune
Alveolar macrophages are epigenetically altered after inflammation, leading to long-term lung immunoparalysis
Nat Immunol. 2020 Jun;21(6):636-648. Epub 2020 May 18. doi: 10.1038/s41590-020-0673-x

Carolane Seiller, Sophie Maiga, Cyrille Touzeau, Céline Bellanger, Charlotte Kervoëlen, Géraldine Descamps, Laurent Maillet, Philippe Moreau, Catherine Pellat-Deceunynck, Patricia Gomez-Bougie, Martine Amiot
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 Dis. 2020 May 5;11(5):316. doi: 10.1038/s41419-020-2505-1

Morgane Frapin, Simon Guignard, Dimitri Meistermann, Isabelle Grit, Valentine S. Moullé, Vincent Paillé, Patricia Parnet, Valérie Amarger
Maternal Protein Restriction in Rats Alters the Expression of Genes Involved in Mitochondrial Metabolism and Epitranscriptomics in Fetal Hypothalamus
Nutrients. 2020 May 19;12(5):E1464. doi: 10.3390/nu12051464

Aude Saint Pierre, Joanna Giemza, Isabel Alves, Matilde Karakachoff, Marinna Gaudin, Philippe Amouyel, Jean-François Dartigues, Christophe Tzourio, Martial Monteil, Pilar Galan, Serge Hercberg, Iain Mathieson, Richard Redon, Emmanuelle Génin, Christian Dina
The Genetic History of France 
Eur J Hum Genet. 2020 Feb 10. doi: 10.1038/s41431-020-0604-1 

Thu Ha Pham, Lecomte S, Le Guevel R, Lardenois A, Evrard B, Chalmel F, Ferriere F, Balaguer P, Efstathiou T, Pakdel F
Characterization of Glyceollins as Novel Aryl Hydrocarbon Receptor Ligands and Their Role in Cell Migration
International Journal of Molecular Sciences, 2020, 21, 1368. doi: 10.3390/ijms21041368

Rabé M, Dumont S, Álvarez-Arenas A, Janati H, Belmonte-Beitia J, Calvo G, 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, Gratas C, Vallette F
Identification of a transient state during the acquisition of temozolomide resistance in glioblastoma
Cell Death & Disease, volume 11, 2020. doi: 10.1038/s41419-019-2200-2

2019
 
Fatima-Zahra Boujdad, Alban Gaignard, Mario Südholt, Wilmer Garzón-Alfonso, Luis Daniel Benavides Navarro, Richard Redon
On distributed collaboration for biomedical analyses
CCGrid-Life 2019 Workshop on Clusters, Clouds and Grids for Life Sciences, May 2019, Larnaca, Cyprus. pp.1-10, doi:10.1109/CCGRID.2019.00079

Maxime Folschette, Kirsley Chennen, Alban Gaignard, Richard Redon, Hala Skaf-Molli, et al.
INEX-MED: a Knowledge Graph to explore and link heterogeneous bio-medical data
JOBIM 2019, Jul 2019, Nantes, France. https://hal.archives-ouvertes.fr/hal-02330809v1

Anass Nouri, Florent Autrusseau, Romain Bourcier, Alban Gaignard, Vincent l'Allinec, et al.
3D bifurcations characterization for intra-cranial aneurysms prediction
SPIE Medical Imaging, Feb 2019, San Diego, CA, United States. doi:10.1117/12.2504626

Montassier E, Al-Ghalith G, Mathé C, Le Bastard Q, Douillard V, Garnier A, Guimon R, Raimondeau B, Touchefeu Y, Duchalais E, Vince N, Limou S, Gourraud PA, Laplaud D, Nicot A, Soulillou JP, Berthelot L
Distribution of Bacterial α1,3-Galactosyltransferase Genes in the Human Gut Microbiome
Front Immunol. 2019; 10: 3000. doi: 10.3389/fimmu.2019.03000

Le Bastard Q, Vangay P, Batard E, Knights D, Montassier E
US immigration is associated with rapid and persistent acquisition of antibiotic resistance genes in the gut
Clinical Infectious Diseases (Nov 2019). doi: 10.1093/cid/ciz1087

Nadjet Belbachir, Vincent Portero, Zeina R Al Sayed, Jean-Baptiste Gourraud, Florian Dilasser, Laurence Jesel, Hongchao Guo, Haodi Wu, Nathalie Gaborit, Christophe Guilluy
RRAD mutation causes electrical and cytoskeletal defects in cardiomyocytes derived from a familial case of Brugada syndrome
European Heart Journal, Volume 40, Issue 37, 1 October 2019, Pages 3081–3094. doi:10.1093/eurheartj/ehz308

Leroy T, Louvet J-M, Lalanne C,Le Provost G, Labadie K, Aury J-M, Delzon S, Plomion C, Kremer A
Adaptive introgression as a driver of local adaptation to climate in European white oaks
New Phytologist (2019). doi: 10.1111/nph.16095

Leroy T, Rougemont Q, Dupouey JL, Bodenes C, Lalanne C, Belser C, Labadie K, Le Provost G, Aury JM, Kremer A, Plomion C
Massive postglacial gene flow between European white oaks uncovered genes underlying species barriers
New Phytologist (2019). doi: 10.1111/nph.16039

Leveque X, Hochane M, Geraldo F, Dumont S, Gratas C, Oliver L, Gaignier C, Trichet V, Layrolle P, Heymann D, Herault O, Vallette F, Olivier C
Low‐dose pesticide mixture induces accelerated mesenchymal stem cells aging in vitro
STEM CELLS 9999:00–00. doi: 10.1002/stem.3014

Thériault S, Dina C, Messika-Zeitoun D, Le Scouarnec S, Capoulade R, Gaudreault N, Rigade S, Li Z, Simonet F, Lamontagne M, Clavel MA, Arsenault B, Boureau A-S, Lecointe S, Baron E, Bonnaud S, Karakachoff M, Charpentier E, Fellah I, Roussel J-C, Verhoye JP, Baufreton C, Probst V, Roussel R, D.E.S.I.R. Study Group, Redon R, Dagenais F, Pibarot P, Mathieu P, Le Tourneau T, Bossé Y, JJ Schott
Genetic association analyses highlight IL6, ALPL, and NAV1 as three new susceptibility genes underlying calcific aortic valve stenosis
Circulation: Genomic and Precision Medicine. 2019;12. doi: 10.1161/CIRCGEN.119.002617

Guimbretiere G, Le Scouarnec S, Rigade S, Boureau AS, Cueff C, Capoulade R, Dina C, Mérot J, Schott JJ, Le Tourneau T
Phenotypic and genotypic approach of a large family with early onset tricuspid aortic valve sclerosis-stenosis: A multimodality evaluation
Archives of Cardiovascular Diseases Supplements, January 2019  11(1):66-67. doi: 10.1016/j.acvdsp.2018.10.145