Papers including work performed at the Genomics Platform

Alphabetical order of first authors names

• Albert B, Kos-Braun IC, Henras AK, Dez C, Rueda MP, Zhang X, Gadal O, Kos M, Shore D. A ribosome assembly stress response regulates transcription to maintain proteome homeostasis. Elife. 2019 May 24;8:e45002.  > Pubmed
• Albert B, Tomassetti S, Gloor Y, Dilg D, Mattarocci S, Kubik S, Hafner L, Shore D. Sfp1 regulates transcriptional networks driving cell growth and division through multiple promoter-binding modes. Genes Dev. 2019 Mar 1;33(5-6):288-293.  > Pubmed
• Amirsoleimani A, Brion GM, Diene SM, François P, Richard EM. Prevalence and characterization of Staphylococcus aureus in wastewater treatment plants by whole genomic sequencing. Water Res. 2019 Jul 1;158:193-202.  > Pubmed
• Bronesky D, Desgranges E, Corvaglia A, François P, Caballero CJ, Prado L, Toledo-Arana A, Lasa I, Moreau K, Vandenesch F, Marzi S, Romby P, Caldelari I. A multifaceted small RNA modulates gene expression upon glucose limitation in Staphylococcus aureus. EMBO J. 2019 Mar 15;38(6). pii: e99363.  > Pubmed
• Cederroth CR, Park JS, Basinou V, Weger BD, Tserga E, Sarlus H, Magnusson AK, Kadri N, Gachon F, Canlon B. Circadian regulation of cochlear sensitivity to noise by circulating glucocorticoids. Curr Biol. 2019 Aug 5;29(15):2477-2487.e6.  > Pubmed
• Cordey S, Laubscher F, Hartley MA, Junier T, Pérez-Rodriguez FJ, Keitel K, Vieille G, Samaka J, Mlaganile T, Kagoro F, Boillat-Blanco N, Mbarack Z, Docquier M, Brito F, Eibach D, May J, Sothmann P, Aldrich C, Lusingu J, Tapparel C, D'Acremont V, Kaiser L. Detection of dicistroviruses RNA in blood of febrile Tanzanian children. Emerg Microbes Infect. 2019;8(1):613-623.  > Pubmed
• Dahyot S, Lebeurre J, Laumay F, Argemi X, Dubos C, Lemée L, Prévost G, François P, Pestel-Caron M. fbl-typing of Staphylococcus lugdunensis: a frontline tool for epidemiological studies, but not predictive of fibrinogen binding ability. Front Microbiol. 2019 May 17;10:1109.  > Pubmed
• Darbellay F, Bochaton C, Lopez-Delisle L, Mascrez B, Tschopp P, Delpretti S, Zakany J, Duboule D. The constrained architecture of mammalian Hox gene clusters. Proc Natl Acad Sci U S A. 2019 Jul 2;116(27):13424-13433.  > Pubmed
• Daull P, Barabino S, Feraille L, Kessal K, Docquier M, Parsadaniantz SM, Baudouin C, Garrigue JS. Modulation of inflammation-related genes in the cornea of a mouse model of dry eye upon treatment with cyclosporine eye drops. Curr Eye Res. 2019 May;44(5):476-485.  > Pubmed
• Delaney K, Strobino M, Wenda JM, Pankowski A, Steiner FA. H3.3K27M-induced chromatin changes drive ectopic replication through misregulation of the JNK pathway in C. elegans. Nat Commun. 2019 Jun 7;10(1):2529.  > Pubmed
• Furuyama K, Chera S, van Gurp L, Oropeza D, Ghila L, Damond N, Vethe H, Paulo JA, Joosten AM, Berney T, Bosco D, Dorrell C, Grompe M, Ræder H, Roep BO, Thorel F, Herrera PL. Diabetes relief in mice by glucose-sensing insulin-secreting human α-cells. Nature. 2019 Mar;567(7746):43-48.  > Pubmed
• Garcia A, Dunoyer-Geindre S, Zapilko V, Nolli S, Reny JL, Fontana P. Functional validation of microRNA-126-3p as a platelet reactivity regulator using human haematopoietic stem cells. Thromb Haemost. 2019 Feb;119(2):254-263.  > Pubmed
• Klingler E, De la Rossa A, Fièvre S, Devaraju K, Abe P, Jabaudon D. A translaminar genetic logic for the circuit identity of intracortically projecting neurons. Curr Biol. 2019 Jan 21;29(2):332-339.e5.  > Pubmed
• Kubik S, Bruzzone MJ, Challal D, Dreos R, Mattarocci S, Bucher P, Libri D, Shore D. Opposing chromatin remodelers control transcription initiation frequency and start site selection. Nat Struct Mol Biol. 2019 Aug;26(8):744-754.  > Pubmed
• Laumay F, Corvaglia AR, Diene SM, Girard M, Oechslin F, van der Mee-Marquet N, Entenza JM, François P. Temperate prophages increase bacterial adhesin expression and virulence in an experimental model of endocarditis due to Staphylococcus aureus from the CC398 lineage. Front Microbiol. 2019 Apr 24;10:742.  > Pubmed
• Liang H, Kessal K, Rabut G, Daull P, Garrigue JS, Melik Parsadaniantz S, Docquier M, Baudouin C, Brignole-Baudouin F. Correlation of clinical symptoms and signs with conjunctival gene expression in primary Sjögren syndrome dry eye patients. Ocul Surf. 2019 Jul;17(3):516-525.  > Pubmed
• Lo Giudice Q, Leleu M, La Manno G, Fabre PJ. Single-cell transcriptional logic of cell-fate specification and axon guidance in early born retinal neurons. Development. 2019 Sep 9;146(17). pii: dev178103.  > Pubmed
• Macheret M, Halazonetis TD. Monitoring early S-phase origin firing and replication fork movement by sequencing nascent DNA from synchronized cells. Nat Protoc. 2019 Jan;14(1):51-67.  > Pubmed
• Martí i Líndez AA, Dunand-Sauthier I, Conti M, Gobet F, Núñez N, Hannich JT, Riezman H, Geiger R, Piersigilli A, Hahn K, Lemeille S, Becher B, De Smedt T, Hugues S, Reith W. Mitochondrial arginase-2 is a cell-autonomous regulator of CD8+ T cell function and antitumor efficacy. JCI Insight. 2019 Nov 21;4(24):e132975.  > Pubmed
• Mikheyeva IV, Thomas JM, Kolar SL, Corvaglia AR, Gaϊa N, Leo S, Francois P, Liu GY, Rawat M, Cheung AL. YpdA, a putative bacillithiol disulfide reductase, contributes to cellular redox homeostasis and virulence in Staphylococcus aureus. Mol Microbiol. 2019 Apr;111(4):1039-1056.  > Pubmed
• Mishra S, Bernal C, Silvano M, Anand S, Ruiz I Altaba A. The protein secretion modulator TMED9 drives CNIH4/TGFα/GLI signaling opposing TMED3-WNT-TCF to promote colon cancer metastases. Oncogene. 2019 Jul;38(29):5817-5837.  > Pubmed
• Niven J, Madelon N, Page N, Caruso A, Harlé G, Lemeille S, Seemayer CA, Hugues S, Gannagé M. Macroautophagy in dendritic cells controls the homeostasis and stability of regulatory T cells. Cell Rep. 2019 Jul 2;28(1):21-29.e6.  > Pubmed
• Oberst P, Fièvre S, Baumann N, Concetti C, Bartolini G, Jabaudon D. Temporal plasticity of apical progenitors in the developing mouse neocortex. Nature. 2019 Sep;573(7774):370-374.  > Pubmed
• Panousis NI, Bertsias GK, Ongen H, Gergianaki I, Tektonidou MG, Trachana M, Romano-Palumbo L, Bielser D, Howald C, Pamfil C, Fanouriakis A, Kosmara D, Repa A, Sidiropoulos P, Dermitzakis ET, Boumpas DT. Combined genetic and transcriptome analysis of patients with SLE: distinct, targetable signatures for susceptibility and severity. Ann Rheum Dis. 2019 Aug;78(8):1079-1089.  > Pubmed
• Pedretti S, Brulhart-Meynet MC, Montecucco F, Lecour S, James RW, Frias MA. HDL protects against myocardial ischemia reperfusion injury via miR-34b and miR-337 expression which requires STAT3. PLoS One. 2019 Jun 20;14(6):e0218432.  > Pubmed
• Rodríguez-Carballo E, Lopez-Delisle L, Yakushiji-Kaminatsui N, Ullate-Agote A, Duboule D. Impact of genome architecture on the functional activation and repression of Hox regulatory landscapes. BMC Biol. 2019 Jul 12;17(1):55.  > Pubmed
• Rousset F, Salmon P, Bredl S, Cherpin O, Coelho M, Myburgh R, Alessandrini M, Perny M, Roccio M, Speck RF, Senn P, Krause KH. Optimizing synthetic miRNA minigene architecture for efficient miRNA hairpin concatenation and multi-target gene knockdown. Mol Ther Nucleic Acids. 2019 Mar 1;14:351-363.  > Pubmed
• Schibler M, Brito F, Zanella M-C, Zdobnov EM, Laubscher F, L’Huillier AG, Ambrosioni J, Wagner N, Posfay-Barbe KM, Docquier M, Schiffer E, Savoldelli GL, Fournier R, Lenggenhager L, Cordey S, Kaiser L. Viral sequences detection by high-throughput sequencing in cerebrospinal fluid of individuals with and without central nervous system disease. Genes (Basel). 2019 Aug 19;10(8). pii: E625.  > Pubmed
• Steinbach K, Vincenti I, Egervari K, Kreutzfeldt M, van der Meer F, Page N, Klimek B, Rossitto-Borlat I, Di Liberto G, Muschaweckh A, Wagner I, Hammad K, Stadelmann C, Korn T, Hartley O, Pinschewer DD, Merkler D. Brain-resident memory T cells generated early in life predispose to autoimmune disease in mice. Sci Transl Med. 2019 Jun 26;11(498):eaav5519.  > Pubmed
• Stévant I, Kühne F, Greenfield A, Chaboissier MC, Dermitzakis ET, Nef S. Dissecting cell lineage specification and sex fate determination in gonadal somatic cells using single-cell transcriptomics. Cell Rep. 2019 Mar 19;26(12):3272-3283.e3.  > Pubmed
• Telley L, Agirman G, Prados J, Amberg N, Fièvre S, Oberst P, Bartolini G, Vitali I, Cadilhac C, Hippenmeyer S, Nguyen L, Dayer A, Jabaudon D. Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex. Science. 2019 May 10;364(6440):eaav2522.  > Pubmed
• Trachsel E, Redder P, Linder P, Armitano J. Genetic screens reveal novel major and minor players in magnesium homeostasis of Staphylococcus aureus. PLoS Genet. 2019 Aug 15;15(8):e1008336.  > Pubmed
• Varum S, Baggiolini A, Zurkirchen L, Atak ZK, Cantù C, Marzorati E, Bossart R, Wouters J, Häusel J, Tuncer E, Zingg D, Veen D, John N, Balz M, Levesque MP, Basler K, Aerts S, Zamboni N, Dummer R, Sommer L. Yin Yang 1 orchestrates a metabolic program required for both neural crest development and melanoma formation. Cell Stem Cell. 2019 Apr 4;24(4):637-653.e9.  > Pubmed
• Vogg MC, Beccari L, Iglesias Ollé L, Rampon C, Vriz S, Perruchoud C, Wenger Y, Galliot B. An evolutionarily-conserved Wnt3/β-catenin/Sp5 feedback loop restricts head organizer activity in Hydra. Nat Commun. 2019 Jan 18;10(1):312.  > Pubmed
• Vono M, Eberhardt CS, Auderset F, Mastelic-Gavillet B, Lemeille S, Christensen D, Andersen P, Lambert PH, Siegrist CA. Maternal antibodies inhibit neonatal and infant responses to vaccination by shaping the early-life B cell repertoire within germinal centers. Cell Rep. 2019 Aug 13;28(7):1773-1784.e5.  > Pubmed
• Vu DL, Cordey S, Simonetta F, Brito F, Docquier M, Turin L, van Delden C, Boely E, Dantin C, Pradier A, Roosnek E, Chalandon Y, Zdobnov EM, Masouridi-Levrat S, Kaiser L. Human pegivirus persistence in the human blood virome after allogeneic haematopoietic stem cell transplantation. Clin Microbiol Infect. 2019 Feb;25(2):225-232.  > Pubmed