2022

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

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


2018

Tessoulin B, Moreau-Aubry A, Descamps G, Gomez-Bougie P, Maïga S, Gaignard A, Chiron D, Ménoret E, Le Gouill S, Moreau P, Amiot M, Pellat-Deceunynck C
Whole-exon sequencing of human myeloma cell lines shows mutations related to myeloma patients at relapse with major hits in the DNA regulation and repair pathways
J Hematol Oncol. 2018 Dec 13;11(1):137 | doi: 10.1186/s13045-018-0679-0
 
Persyn E, Redon R, Bellanger L, Dina C
The impact of a fine-scale population stratification on rare variant association test results
PLOS One 13(12): e0207677, December 2018 | doi: https://doi.org/10.1371/journal.pone.0207677

M Lenglet, F Robriquet, K Schwarz, C Camps, A Couturier, D Hoogewijs, A Buffet, S J. L. Knight, S Gad, S Couvé, F Chesnel, M Pacault, P Lindenbaum, S Job, S Dumont, T Besnard, M Cornec, H Dreau, M Pentony, E Kvikstad, S Deveaux, N Burnichon, S Ferlicot, M Vilaine, JM Mazzella, F Airaud, C Garrec, L Heidet, S Irtan, E Mantadakis, K Bouchireb, K-M Debatin, R Redon, S Bezieau, B Bressac-de Paillerets, BT Teh, F Girodon, M-L Randi, M Caterina Putti, V Bours, R Van Wijk, J R. Göthert, A Kattamis, N Janin, C Bento, J C. Taylor, Y Arlot-Bonnemains, S Richard, A-P Gimenez-Roqueplo, H Cario and B Gardie
Identification of a new VHL exon and complex splicing alterations in familial erythrocytosis or von Hippel-Lindau disease
Blood 2018 132:469-483, September 2018 | doi: https://doi.org/10.1182/blood-2018-03-838235

Eric Charpentier, Audrey Bihouee, Dimitri Meistermann, Stephanie Kilens, Lea Flippe, Solenne Dumont, Audrey Donnart,Marine Cornec, Laurent David, Richard Redon
3’seq-RP : A low cost high throughput digital sequencing technique to evaluate gene expression profiles
Journées Ouvertes en BioInformatique et Mathématiques (JOBIM2018, Poster).
 
Chebouba L, Boughaci D, Guziolowski C
Proteomics Versus Clinical Data and Stochastic Local Search Based Feature Selection for Acute Myeloid Leukemia Patients' Classification
Journal of Medical Systems, 2018https://doi.org/10.1007/s10916-018-0972-z

Dumont S, Le Pennec S, Donnart A, Teusan R, Steenman M, Chevalier C, Houlgatte R and Savagner F
Transcriptional orchestration of mitochondrial homeostasis in a cellular model of PGC-1-related coactivator-dependent thyroid tumor
Oncotarget, 2018 Mar 23;9(22):15883-15894 | https://doi.org/10.18632/oncotarget.24633 

Dinka Mandakovic, Claudia Rojas, Jonathan Maldonado, Mauricio Latorre, Dante Travisany, Erwan Delage, Audrey Bihouée, Géraldine Jean, Francisca P. Díaz, Beatriz Fernández-Gómez, Pablo Cabrera, Alexis Gaete, Claudio Latorre, Rodrigo A. Gutiérrez, Alejandro Maass, Verónica Cambiazo, Sergio A. Navarrete, Damien Eveillard & Mauricio González
Structure and co-occurrence patterns in microbial communities under acute environmental stress reveal ecological factors fostering resilience
Scientific Reports volume 8, Article number: 5875 (2018) | https://doi.org/10.1038/s41598-018-23931-0

L Chebouba, B Miannay, D Boughaci, C Guziolowski
Discriminate the response of Acute Myeloid Leukemia patients to treatment by using proteomics data and Answer Set Programming
BMC Bioinformatics, March 2018 19(Suppl 2):59 | https://doi.org/10.1186/s12859-018-2034-4

Espitia O, Chatelais M, Steenman M, Charrier C, Maurel B, Georges S, Houlgatte R, Verrecchia F, Ory B, Lamoureux F, Heymann D, Gouëffic Y, Quillard T
Implication of molecular vascular smooth muscle cell heterogeneity among arterial beds in arterial calcification.
PLOS One, January 26, 2018 | https://doi.org/10.1371/journal.pone.0191976

Kilens S, Meistermann D, Moreno D, Chariau C, Gaignerie A, Reignier A, Lelièvre Y, Casanova M, Vallot C, Nedellec S, Flippe L, Firmin J, Song J, Charpentier E, Lammers J, Donnart A, Marec N, Deb W, Bihouée A, Le Caignec C, Pecqueur C, Redon R, Barrière P, Bourdon J, Pasque V, Soumillon M, Mikkelsen TS, Rougeulle C, Fréour T, David L and The Milieu Intérieur Consortium
Parallel derivation of isogenic human primed and naive induced pluripotent stem cells.
Nat Commun. 2018 Jan 24;9(1):360 | https://doi.org/10.1038/s41467-017-02107-w

S. Bézie, D. Meistermann, L. Boucault, S. Kilens, J. Zoppi, E. Autrusseau, A. Donnart, V. Nerrière-Daguin, F. Bellier-Waast, E. Charpentier, F. Duteille, L. David, I. Anegon and C. Guillonneau
Ex vivo expanded human non-cytotoxic CD8+CD45RClow/- tregs efficiently delay skin graft rejection and GVHD in humanized mice.
Front Immunol, 24 January 2018 | https://doi.org/10.3389/fimmu.2017.02014

R Danger, PJ Royer, D Reboulleau, E Durand, J Loy, A Tissot, P Lacoste, A Roux, M Reynaud-Gaubert, C Gomez, R Kessler, S Mussot, C Dromer, O Brugière, JF Mornex, R Guillemain, M Dahan, C Knoop, K Botturi, A Foureau, C Pison, A Koutsokera, L Nicod, S Brouard, A Magnan and  The COLT and SysCLAD Consortia
Blood Gene Expression Predicts Bronchiolitis Obliterans Syndrome
Front. Immunol., 11 January 2018 | https://doi.org/10.3389/fimmu.2017.01841
 
Bourcier R, Le Scouarnec S, Bonnaud S, Karakachoff M, Bourcereau E, Heurtebise-Chrétien S, Menguy C, Dina C, Simonet F, Moles A, Lenoble C, Lindenbaum P, Chatel S, Isidor B, Génin E, Deleuze JF, Schott JJ
Rare Coding Variants in ANGPTL6 Are Associated with Familial Forms of Intracranial Aneurysm
The American Journal of Human Genetics, Volume 102, Issue 1, 4 January 2018, Pages 133–141 | https://doi.org/10.1016/j.ajhg.2017.12.006