Publications

Publications 2017

Papers including work performed in the frame of iGE3

Alphabetical order of first authors’ names

  • Boquett JA, Nunes JM, Buhler S, de Oliveira MZ, Jobim LF, Jobim M, Fagundes NJ, Schüler-Faccini L, Sanchez-Mazas A. The HLA-A, -B and -DRB1 polymorphism in a large dataset of South Brazil bone marrow donors from Rio Grande do Sul. HLA. 2017 Jan;89(1):29-38. ► Pubmed
  • Brown AA, Viñuela A, Delaneau O, Spector TD, Small KS, Dermitzakis ET. Predicting causal variants affecting expression by using whole-genome sequencing and RNA-seq from multiple human tissues. Nat Genet. 2017 Dec;49(12):1747-1751. ► Pubmed
  • Bryois J, Buil A, Ferreira PG, Panousis NI, Brown AA, Viñuela A, Planchon A, Bielser D, Small K, Spector T, Dermitzakis ET. Time-dependent genetic effects on gene expression implicate aging processes. Genome Res. 2017 Apr;27(4):545-552. ► Pubmed
  • Chahtane H, Kim W, Lopez-Molina L. Primary seed dormancy: a temporally multilayered riddle waiting to be unlocked. J Exp Bot. 2017 Feb 1;68(4):857-869. ► Pubmed
  • Damond N, Thorel F, Kim SK, Herrera PL. Dnmt1 activity is dispensable in δ-cells but is essential for α-cell homeostasis. Int J Biochem Cell Biol. 2017 Jul;88:226-235. ► Pubmed
  • Delaneau O, Ongen H, Brown AA, Fort A, Panousis NI, Dermitzakis ET. A complete tool set for molecular QTL discovery and analysis. Nat Commun. 2017 May 18;8:15452. ► Pubmed
  • Dietschi Q, Tuberosa J, Rösingh L, Loichot G, Ruedi M, Carleton A, Rodriguez I. Evolution of immune chemoreceptors into sensors of the outside world. Proc Natl Acad Sci U S A. 2017 Jul 11;114(28):7397-7402. ► Pubmed
  • Ekundayo B, Richmond TJ, Schalch T. Capturing structural heterogeneity in chromatin fibers. J Mol Biol. 2017 Oct 13;429(20):3031-3042. ► Pubmed
  • Fabbiano S, Suárez-Zamorano N, Trajkovski M. Host-microbiota mutualism in metabolic diseases. Front Endocrinol (Lausanne). 2017 Oct 4;8:267. ► Pubmed
  • Fort A, Panousis NI, Garieri M, Antonarakis SE, Lappalainen T, Dermitzakis ET, Delaneau O. MBV: a method to solve sample mislabeling and detect technical bias in large combined genotype and sequencing assay datasets. Bioinformatics. 2017 Jun 15;33(12):1895-1897. ► Pubmed
  • Gali VK, Balint E, Serbyn N, Frittmann O, Stutz F, Unk I. Translesion synthesis DNA polymerase η exhibits a specific RNA extension activity and a transcription-associated function. Sci Rep. 2017 Oct 12;7(1):13055. ► Pubmed
  • Galliot B, Crescenzi M, Jacinto A, Tajbakhsh S. Trends in tissue repair and regeneration. Development. 2017 Feb 1;144(3):357-364. ► Pubmed
  • Garieri M, Delaneau O, Santoni F, Fish RJ, Mull D, Carninci P, Dermitzakis ET, Antonarakis SE, Fort A. The effect of genetic variation on promoter usage and enhancer activity. Nat Commun. 2017 Nov 7;8(1):1358. ► Pubmed
  • GTEx Consortium; Laboratory, Data Analysis & Coordinating Center (LDACC)—Analysis Working Group; Statistical Methods groups—Analysis Working Group; Enhancing GTEx (eGTEx) groups; NIH Common Fund; NIH/NCI; NIH/NHGRI; NIH/NIMH; NIH/NIDA; Biospecimen Collection Source Site—NDRI; Biospecimen Collection Source Site—RPCI; Biospecimen Core Resource—VARI; Brain Bank Repository—University of Miami Brain Endowment Bank; Leidos Biomedical—Project Management; ELSI Study; Genome Browser Data Integration & Visualization—EBI; Genome Browser Data Integration & Visualization—UCSC Genomics Institute, University of California Santa Cruz; Lead analysts:; Laboratory, Data Analysis & Coordinating Center (LDACC):; NIH program management:; Biospecimen collection:; Pathology:; eQTL manuscript working group:, Battle A, Brown CD, Engelhardt BE, Montgomery SB. Genetic effects on gene expression across human tissues. Nature. 2017 Oct 11;550(7675):204-213. ► Pubmed
  • Guipponi M, Santoni F, Schneider M, Gehrig C, Bustillo XB, Kates WR, Morrow B, Armando M, Vicari S, Sloan-Béna F, Gagnebin M, Shashi V, Hooper SR, Eliez S, Antonarakis SE. No evidence for the presence of genetic variants predisposing to psychotic disorders on the non-deleted 22q11.2 allele of VCFS patients. Transl Psychiatry. 2017 Feb 21;7(2):e1039. ► Pubmed
  • Guri Y, Colombi M, Dazert E, Hindupur SK, Roszik J, Moes S, Jenoe P, Heim MH, Riezman I, Riezman H, Hall MN. mTORC2 promotes tumorigenesis via lipid synthesis. Cancer Cell. 2017 Dec 11;32(6):807-823.e12. ► Pubmed
  • Hallez R, Delaby M, Sanselicio S, Viollier PH. Hit the right spots: cell cycle control by phosphorylated guanosines in alphaproteobacteria. Nat Rev Microbiol. 2017 Mar;15(3):137-148. ► Pubmed
  • Jacovetti C, Rodriguez-Trejo A, Guay C, Sobel J, Gattesco S, Petrenko V, Saini C, Dibner C, Regazzi R. MicroRNAs modulate core-clock gene expression in pancreatic islets during early postnatal life in rats. Diabetologia. 2017 Oct;60(10):2011-2020. ► Pubmed
  • Jardim de Queiroz L, Torrente-Vilara G, Quilodran C, Rodrigues da Costa Doria C, Montoya-Burgos JI. Multifactorial genetic divergence processes drive the onset of speciation in an Amazonian fish. PLoS One. 2017 Dec 20;12(12):e0189349. ► Pubmed
  • Karuppasamy M, Kusmider B, Oliveira TM, Gaubitz C, Prouteau M, Loewith R, Schaffitzel C. Cryo-EM structure of Saccharomyces cerevisiae target of rapamycin complex 2. Nat Commun. 2017 Nov 23;8(1):1729. ► Pubmed
  • Kassem S, Villanyi Z, Collart MA. Not5-dependent co-translational assembly of Ada2 and Spt20 is essential for functional integrity of SAGA. Nucleic Acids Res. 2017 Feb 17;45(3):1186-1199. ► Pubmed
  • Kubik S, Bruzzone MJ, Albert B, Shore D. A reply to “MNase-Sensitive Complexes in Yeast: Nucleosomes and Non-histone Barriers,” by Chereji et al. Mol Cell. 2017 Feb 2;65(3):578-580. ► Pubmed
  • Kubik S, Bruzzone MJ, Shore D. Establishing nucleosome architecture and stability at promoters: Roles of pioneer transcription factors and the RSC chromatin remodeler. Bioessays. 2017 May;39(5). ► Pubmed
  • Kubik S, Bruzzone MJ, Shore D. TFIID or not TFIID, a continuing transcriptional SAGA. EMBO J. 2017 Feb 1;36(3):248-249. ► Pubmed
  • Lau P, Cordey S, Brito F, Tirefort D, Petty TJ, Turin L, Guichebaron A, Docquier M, Zdobnov EM, Waldvogel-Abramowski S, Lecompte T, Kaiser L, Preynat-Seauve O. Metagenomics analysis of red blood cell and fresh-frozen plasma units. Transfusion. 2017 Jul;57(7):1787-1800. ► Pubmed
  • Lee D, Creed M, Jung K, Stefanelli T, Wendler DJ, Oh WC, Mignocchi NL, Lüscher C, Kwon HB. Temporally precise labeling and control of neuromodulatory circuits in the mammalian brain. Nat Methods. 2017 May;14(5):495-503. ► Pubmed
  • Liu Y, Borel C, Li L, Müller T, Williams EG, Germain PL, Buljan M, Sajic T, Boersema PJ, Shao W, Faini M, Testa G, Beyer A, Antonarakis SE, Aebersold R. Systematic proteome and proteostasis profiling in human Trisomy 21 fibroblast cells. Nat Commun. 2017 Oct 31;8(1):1212. ► Pubmed
  • Loizides-Mangold U, Perrin L, Vandereycken B, Betts JA, Walhin JP, Templeman I, Chanon S, Weger BD, Durand C, Robert M, Paz Montoya J, Moniatte M, Karagounis LG, Johnston JD, Gachon F, Lefai E, Riezman H, Dibner C. Lipidomics reveals diurnal lipid oscillations in human skeletal muscle persisting in cellular myotubes cultured in vitro. Proc Natl Acad Sci U S A. 2017 Oct 10;114(41):E8565-E8574. ► Pubmed
  • Loubéry S, Daeden A, Seum C, Holtzer L, Moraleda A, Damond N, Derivery E, Schmidt T, Gonzalez-Gaitan M. Sara phosphorylation state controls the dispatch of endosomes from the central spindle during asymmetric division. Nat Commun. 2017 Jun 6;8:15285. ► Pubmed
  • Manukyan L, Montandon SA, Fofonjka A, Smirnov S, Milinkovitch MC. A living mesoscopic cellular automaton made of skin scales. Nature. 2017 Apr 12;544(7649):173-179. ► Pubmed
  • Mattarocci S, Reinert JK, Bunker RD, Fontana GA, Shi T, Klein D, Cavadini S, Faty M, Shyian M, Hafner L, Shore D, Thomä NH, Rass U. Rif1 maintains telomeres and mediates DNA repair by encasing DNA ends. Nat Struct Mol Biol. 2017 Jul;24(7):588-595. ► Pubmed
  • Ongen H, Brown AA, Delaneau O, Panousis NI, Nica AC; GTEx Consortium, Dermitzakis ET. Estimating the causal tissues for complex traits and diseases. Nat Genet. 2017 Dec;49(12):1676-1683. ► Pubmed
  • Petrenko V, Dibner C. Circadian orchestration of insulin and glucagon release. Cell Cycle. 2017 Jun 18;16(12):1141-1142. ► Pubmed
  • Petrenko V, Gosmain Y, Dibner C. High-resolution recording of the circadian oscillator in primary mouse α- and β-cell culture. Front Endocrinol (Lausanne). 2017 Apr 7;8:68. ► Pubmed
  • Petrenko V, Saini C, Giovannoni L, Gobet C, Sage D, Unser M, Heddad Masson M, Gu G, Bosco D, Gachon F, Philippe J, Dibner C. Pancreatic α- and β-cellular clocks have distinct molecular properties and impact on islet hormone secretion and gene expression. Genes Dev. 2017 Feb 15;31(4):383-398. ► Pubmed
  • Pino P, Caldelari R, Mukherjee B, Vahokoski J, Klages N, Maco B, Collins CR, Blackman MJ, Kursula I, Heussler V, Brochet M, Soldati-Favre D. A multistage antimalarial targets the plasmepsins IX and X essential for invasion and egress. Science. 2017 Oct 27;358(6362):522-528. ► Pubmed
  • Primo C, Ferri-Blázquez A, Loewith R, Yenush L. Reciprocal regulation of Target of Rapamycin Complex 1 and potassium accumulation. J Biol Chem. 2017 Jan 13;292(2):563-574. ► Pubmed
  • Prouteau M, Desfosses A, Sieben C, Bourgoint C, Lydia Mozaffari N, Demurtas D, Mitra AK, Guichard P, Manley S, Loewith R. TORC1 organized in inhibited domains (TOROIDs) regulate TORC1 activity. Nature. 2017 Oct 12;550(7675):265-269. ► Pubmed
  • Pupo M, Bodmer A, Berto M, Maggiolini M, Dietrich PY, Picard D. A genetic polymorphism repurposes the G-protein coupled and membrane-associated estrogen receptor GPER to a transcription factor-like molecule promoting paracrine signaling between stroma and breast carcinoma cells. Oncotarget. 2017 Jul 18;8(29):46728-46744. ► Pubmed
  • Ranza E, Garcia-Tarodo S, Varvagiannis K, Guipponi M, Lobrinus JA, Bottani A, Kern I, Kurian M, Pittet MP, Antonarakis SE, Fluss J, Korff CM. SERPINI1 pathogenic variants: An emerging cause of childhood-onset progressive myoclonic epilepsy. Am J Med Genet A. 2017 Sep;173(9):2456-2460. ► Pubmed
  • Rivera-Rivera CJ, Montoya-Burgos JI. Trunk dental tissue evolved independently from underlying dermal bony plates but is associated with surface bones in living odontode-bearing catfish. Proc Biol Sci. 2017 Oct 25;284(1865). ► Pubmed
  • Sanchez-Mazas A, Černý V, Di D, Buhler S, Podgorná E, Chevallier E, Brunet L, Weber S, Kervaire B, Testi M, Andreani M, Tiercy JM, Villard J, Nunes JM. The HLA-B landscape of Africa: Signatures of pathogen-driven selection and molecular identification of candidate alleles to malaria protection. Mol Ecol. 2017 Nov;26(22):6238-6252. ► Pubmed
  • Sanchez-Mazas A, Nunes JM, Middleton D, Sauter J, Buhler S, McCabe A, Hofmann J, Baier DM, Schmidt AH, Nicoloso G, Andreani M, Grubic Z, Tiercy JM, Fleischhauer K. Common and well-documented HLA alleles over all of Europe and within European sub-regions: A catalogue from the European Federation for Immunogenetics. HLA. 2017 Feb;89(2):104-113. ► Pubmed
  • Santoni FA, Stamoulis G, Garieri M, Falconnet E, Ribaux P, Borel C, Antonarakis SE. Detection of imprinted genes by single-cell allele-specific gene expression. Am J Hum Genet. 2017 Mar 2;100(3):444-453. ► Pubmed
  • Schalch T, Steiner FA. Structure of centromere chromatin: from nucleosome to chromosomal architecture. Chromosoma. 2017 Aug;126(4):443-455. ► Pubmed
  • Silva NM, Rio J, Currat M. Investigating population continuity with ancient DNA under a spatially explicit simulation framework. BMC Genet. 2017 Dec 15;18(1):114. ► Pubmed
  • Sinturel F, Gerber A, Mauvoisin D, Wang J, Gatfield D, Stubblefield JJ, Green CB, Gachon F, Schibler U. Diurnal oscillations in liver mass and cell size accompany ribosome assembly cycles. Cell. 2017 May 4;169(4):651-663.e14. ► Pubmed
  • Sluysmans S, Vasileva E, Spadaro D, Shah J, Rouaud F, Citi S. The role of apical cell-cell junctions and associated cytoskeleton in mechanotransduction. Biol Cell. 2017 Apr;109(4):139-161. ► Pubmed
  • Spadaro D, Le S, Laroche T, Mean I, Jond L, Yan J, Citi S. Tension-dependent stretching activates ZO-1 to control the junctional localization of its interactors. Curr Biol. 2017 Dec 18;27(24):3783-3795.e8. ► Pubmed
  • Spiljar M, Merkler D, Trajkovski M. The immune system bridges the gut microbiota with systemic energy homeostasis: focus on TLRs, mucosal barrier, and SCFAs. Front Immunol. 2017 Oct 30;8:1353. ► Pubmed
  • Traub S, Meier DT, Schulze F, Dror E, Nordmann TM, Goetz N, Koch N, Dalmas E, Stawiski M, Makshana V, Thorel F, Herrera PL, Böni-Schnetzler M, Donath MY. Pancreatic α cell-derived glucagon-related peptides are required for β cell adaptation and glucose homeostasis. Cell Rep. 2017 Mar 28;18(13):3192-3203. ► Pubmed
  • Ullate-Agote A, Chan YF, Tzika AC. A step-by-step guide to assemble a reptilian genome. Methods Mol Biol. 2017;1650:47-67. ► Pubmed
  • Vasileva E, Sluysmans S, Bochaton-Piallat ML, Citi S. Cell-specific diversity in the expression and organization of cytoplasmic plaque proteins of apical junctions. Ann N Y Acad Sci. 2017 Oct;1405(1):160-176. ► Pubmed
  • Yamada Y, Bhaukaurally K, Madarász TJ, Pouget A, Rodriguez I, Carleton A. Context- and output layer-dependent long-term ensemble plasticity in a sensory circuit. Neuron. 2017 Mar 8;93(5):1198-1212.e5. ► Pubmed
  • Yin R, Ulm R. How plants cope with UV-B: from perception to response. Curr Opin Plant Biol. 2017 Jun;37:42-48. ► Pubmed
  • Zakany J, Darbellay F, Mascrez B, Necsulea A, Duboule D. Control of growth and gut maturation by HoxD genes and the associated lncRNA Haglr. Proc Natl Acad Sci U S A. 2017 Oct 31;114(44):E9290-E9299. ► Pubmed

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