Papers including work performed at the Genomics Platform

Alphabetical order of first authors names

• Bady P, Kurscheid S, Delorenzi M, Gorlia T, van den Bent MJ, Hoang-Xuan K, Vauléon É, Gijtenbeek A, Enting R, Thiessen B, Chinot O, Dhermain F, Brandes AA, Reijneveld JC, Marosi C, Taphoorn MJB, Wick W, von Deimling A, French P, Stupp R, Baumert BG, Hegi ME. The DNA methylome of DDR genes and benefit from RT or TMZ in IDH mutant low-grade glioma treated in EORTC 22033. Acta Neuropathol. 2018 Apr;135(4):601-615.  > Pubmed
• Beccari L, Moris N, Girgin M, Turner DA, Baillie-Johnson P, Cossy AC, Lutolf MP, Duboule D, Arias AM. Multi-axial self-organization properties of mouse embryonic stem cells into gastruloids. Nature. 2018 Oct;562(7726):272-276.  > Pubmed
• Brito F, Cordey S, Delwart E, Deng X, Tirefort D, Lemoine-Chaduc C, Zdobnov E, Lecompte T, Kaiser L, Waldvogel-Abramowski S, Preynat-Seauve O. Metagenomics analysis of the virome of 300 concentrates from a Swiss platelet bank. Vox Sang. 2018 Aug 20;113(6):601-604.  > Pubmed
• Bruzzone MJ, Grünberg S, Kubik S, Zentner GE, Shore D. Distinct patterns of histone acetyltransferase and Mediator deployment at yeast protein-coding genes. Genes Dev. 2018 Sep 1;32(17-18):1252-1265.  > Pubmed
• Chahtane H, Nogueira Füller T, Allard PM, Marcourt L, Ferreira Queiroz E, Shanmugabalaji V, Falquet J, Wolfender JL, Lopez-Molina L. The plant pathogen Pseudomonas aeruginosa triggers a DELLA-dependent seed germination arrest in Arabidopsis. Elife. 2018 Aug 28;7:e37082.  > Pubmed
• Cherkaoui A, Diene SM, Fischer A, Leo S, François P, Schrenzel J. Transcriptional modulation of penicillin-binding protein 1b, outer membrane protein P2 and efflux pump (AcrAB-TolC) during heat stress is correlated to enhanced bactericidal action of imipenem on non-typeable Haemophilus influenzae. Front Microbiol. 2018 Jan 12;8:2676.  > Pubmed
• Cherkaoui A, Gaïa N, Baud D, Leo S, Fischer A, Ruppe E, François P, Schrenzel J. Molecular characterization of fluoroquinolones, macrolides, and imipenem resistance in Haemophilus influenzae: analysis of the mutations in QRDRs and assessment of the extent of the AcrAB-TolC-mediated resistance. Eur J Clin Microbiol Infect Dis. 2018 Nov;37(11):2201-2210.  > Pubmed
• Cigliola V, Ghila L, Thorel F, van Gurp L, Baronnier D, Oropeza D, Gupta S, Miyatsuka T, Kaneto H, Magnuson MA, Osipovich AB, Sander M, Wright CEV, Thomas MK, Furuyama K, Chera S, Herrera PL. Pancreatic islet-autonomous insulin and smoothened-mediated signalling modulate identity changes of glucagon⁺ α-cells. Nat Cell Biol. 2018 Nov;20(11):1267-1277.  > Pubmed
• Cordey S, Hartley MA, Keitel K, Laubscher F, Brito F, Junier T, Kagoro F, Samaka J, Masimba J, Said Z, Temba H, Mlaganile T, Docquier M, Fellay J, Kaiser L, D'Acremont V. Detection of novel astroviruses MLB1 and MLB2 in the sera of febrile Tanzanian children. Emerg Microbes Infect. 2018 Mar 14;7(1):27.  > Pubmed
• Delaney K, Mailler J, Wenda JM, Gabus C, Steiner FA. Differential expression of histone H3.3 genes and their role in modulating temperature stress response in Caenorhabditis elegans. Genetics. 2018 Jun;209(2):551-565.  > Pubmed
• Elias KM, Tsantoulis P, Tille JC, Vitonis A, Doyle LA, Hornick JL, Kaya G, Barnes L, Cramer DW, Puppa G, Stuckelberger S, Hooda J, Dietrich PY, Goggins M, Kerr CL, Birrer M, Hirsch MS, Drapkin R, Labidi-Galy SI. Primordial germ cells as a potential shared cell of origin for mucinous cystic neoplasms of the pancreas and mucinous ovarian tumors. J Pathol. 2018 Dec;246(4):459-469.  > Pubmed
• Essaidi-Laziosi M, Brito F, Benaoudia S, Royston L, Cagno V, Fernandes-Rocha M, Piuz I, Zdobnov E, Huang S, Constant S, Boldi MO, Kaiser L, Tapparel C. Propagation of respiratory viruses in human airway epithelia reveals persistent virus-specific signatures. J Allergy Clin Immunol. 2018 Jun;141(6):2074-2084.  > Pubmed
• Fregni G, Quinodoz M, Möller E, Vuille J, Galland S, Fusco C, Martin P, Letovanec I, Provero P, Rivolta C, Riggi N, Stamenkovic I. Reciprocal modulation of mesenchymal stem cells and tumor cells promotes lung cancer metastasis. EBioMedicine. 2018 Mar;29:128-145.  > Pubmed
• Hafner L, Lezaja A, Zhang X, Lemmens L, Shyian M, Albert B, Follonier C, Nunes JM, Lopes M, Shore D, Mattarocci S. Rif1 binding and control of chromosome-internal DNA replication origins is limited by telomere sequestration. Cell Rep. 2018 Apr 24;23(4):983-992.  > Pubmed
• Kessal K, Liang H, Rabut G, Daull P, Garrigue JS, Docquier M, Melik Parsadaniantz S, Baudouin C, Brignole-Baudouin F. Conjunctival inflammatory gene expression profiling in dry eye disease: correlations with HLA-DRA and HLA-DRB1. Front Immunol. 2018 Oct 15;9:2271.  > Pubmed
• Kubik S, O'Duibhir E, de Jonge WJ, Mattarocci S, Albert B, Falcone JL, Bruzzone MJ, Holstege FCP, Shore D. Sequence-directed action of RSC remodeler and general regulatory factors modulates +1 nucleosome position to facilitate transcription. Mol Cell. 2018 Jul 5;71(1):89-102.e5.  > Pubmed
• Lahlil R, Scrofani M, Barbet R, Tancredi C, Aries A, Hénon P. VSELs maintain their pluripotency and competence to differentiate after enhanced ex vivo expansion. Stem Cell Rev. 2018 Aug;14(4):510-524.  > Pubmed
• Macheret M, Halazonetis TD. Intragenic origins due to short G1 phases underlie oncogene-induced DNA replication stress. Nature. 2018 Mar 1;555(7694):112-116.  > Pubmed
• Manna AC, Kim S, Cengher L, Corvaglia A, Leo S, Francois P, Cheung AL. Small RNA teg49 is derived from a sarA transcript and regulates virulence genes independent of SarA in Staphylococcus aureus. Infect Immun. 2018 Jan 22;86(2).  > Pubmed
• Molinard-Chenu A, Dayer A. The candidate schizophrenia risk gene DGCR2 regulates early steps of corticogenesis. Biol Psychiatry. 2018 Apr 15;83(8):692-706.  > Pubmed
• Page N, Klimek B, De Roo M, Steinbach K, Soldati H, Lemeille S, Wagner I, Kreutzfeldt M, Di Liberto G, Vincenti I, Lingner T, Salinas G, Brück W, Simons M, Murr R, Kaye J, Zehn D, Pinschewer DD, Merkler D. Expression of the DNA-binding factor TOX promotes the encephalitogenic potential of microbe-induced autoreactive CD8⁺ T cells. Immunity. 2018 May 15;48(5):937-950.e8.  > Pubmed
• Sadowski SM, Pusztaszeri M, Brulhart-Meynet MC, Petrenko V, De Vito C, Sobel J, Delucinge-Vivier C, Kebebew E, Regazzi R, Philippe J, Triponez F, Dibner C. Identification of differential transcriptional patterns in primary and secondary hyperparathyroidism. J Clin Endocrinol Metab. 2018 Jun 1;103(6):2189-2198.  > Pubmed
• Sevestre J, Diene SM, Aouiti-Trabelsi M, Deghmane AE, Tournier I, François P, Caron F, Taha MK. Differential expression of hemoglobin receptor, HmbR, between carriage and invasive isolates of Neisseria meningitidis contributes to virulence: lessons from a clonal outbreak. Virulence. 2018 Dec 31;9(1):923-929.  > Pubmed
• Soudet J, Gill JK, Stutz F. Noncoding transcription influences the replication initiation program through chromatin regulation. Genome Res. 2018 Dec;28(12):1882-1893.  > Pubmed
• Stévant I, Neirijnck Y, Borel C, Escoffier J, Smith LB, Antonarakis SE, Dermitzakis ET, Nef S. Deciphering cell lineage specification during male sex determination with single-cell RNA sequencing. Cell Rep. 2018 Feb 6;22(6):1589-1599.  > Pubmed
• van der Mee-Marquet N, Diene SM, Barbera L, Courtier-Martinez L, Lafont L, Ouachée A, Valentin AS, Santos SD, Quentin R, François P. Analysis of the prophages carried by human infecting isolates provides new insight into the evolution of Group B Streptococcus species. Clin Microbiol Infect. 2018 May;24(5):514-521.  > Pubmed
• Vitali I, Fièvre S, Telley L, Oberst P, Bariselli S, Frangeul L, Baumann N, McMahon JJ, Klingler E, Bocchi R, Kiss JZ, Bellone C, Silver DL, Jabaudon D. Progenitor hyperpolarization regulates the sequential generation of neuronal subtypes in the developing neocortex. Cell. 2018 Aug 23;174(5):1264-1276.e15.  > Pubmed
• Yakushiji-Kaminatsui N, Lopez-Delisle L, Bolt CC, Andrey G, Beccari L, Duboule D. Similarities and differences in the regulation of HoxD genes during chick and mouse limb development. PLoS Biol. 2018 Nov 26;16(11):e3000004.  > Pubmed
• Yildiz S, Mazel-Sanchez B, Kandasamy M, Manicassamy B, Schmolke M. Influenza A virus infection impacts systemic microbiota dynamics and causes quantitative enteric dysbiosis. Microbiome. 2018 Jan 10;6(1):9.  > Pubmed