Publications

Publications 2015

Papers including work performed in the frame of iGE3

Alphabetical order of first authors’ names

  • Ardissone S, Viollier PH. Interplay between flagellation and cell cycle control in Caulobacter. Curr Opin Microbiol. 2015 Oct 15;28:83-92. ► Pubmed
  • Bartošová-Sojková P, Oppenheim RD, Soldati-Favre D, Lukeš J. Epicellular apicomplexans: parasites "On the way in". PLoS Pathog. 2015 Sep 24;11(9):e1005080. ► Pubmed
  • Belin D, Plaia G, Boulfekhar Y, Silva F. Escherichia coli SecG is required for residual export mediated by mutant signal sequences and for SecY-SecE complex stability. J Bacteriol. 2015 Feb;197(3):542-52. ► Pubmed
  • Bender T, Pena G, Martinou JC. Regulation of mitochondrial pyruvate uptake by alternative pyruvate carrier complexes. EMBO J. 2015 Apr 1;34(7):911-24. ► Pubmed
  • Borel C, Ferreira PG, Santoni F, Delaneau O, Fort A, Popadin KY, Garieri M, Falconnet E, Ribaux P, Guipponi M, Padioleau I, Carninci P, Dermitzakis ET, Antonarakis SE. Biased allelic expression in human primary fibroblast single cells. Am J Hum Genet. 2015 Jan 8;96(1):70-80. ► Pubmed
  • Brault V, Duchon A, Romestaing C, Sahun I, Pothion S, Karout M, Borel C, Dembele D, Bizot JC, Messaddeq N, Sharp AJ, Roussel D, Antonarakis SE, Dierssen M, Hérault Y. Opposite phenotypes of muscle strength and locomotor function in mouse models of partial trisomy and monosomy 21 for the proximal Hspa13-App region. PLoS Genet. 2015 Mar 24;11(3):e1005062. ► Pubmed
  • Buzgariu W, Al Haddad S, Tomczyk S, Wenger Y, Galliot B. Multi-functionality and plasticity characterize epithelial cells in Hydra. Tissue Barriers. 2015 Jul 15;3(4):e1068908. ► Pubmed
  • Castelnuovo M, Stutz F. Role of chromatin, environmental changes and single cell heterogeneity in non-coding transcription and gene regulation. Curr Opin Cell Biol. 2015 Jun;34:16-22. ► Pubmed
  • Castonguay E, White SA, Kagansky A, St-Cyr DJ, Castillo AG, Brugger C, White R, Bonilla C, Spitzer M, Earnshaw WC, Schalch T, Ekwall K, Tyers M, Allshire RC. Panspecies small-molecule disruptors of heterochromatin-mediated transcriptional gene silencing. Mol Cell Biol. 2015 Feb;35(4):662-74. ► Pubmed
  • Chentouf A, Dahdouh A, Guipponi M, Oubaiche ML, Chaouch M, Hamamy H, Antonarakis SE. Familial epilepsy in Algeria: Clinical features and inheritance profiles. Seizure. 2015 Sep;31:12-8. ► Pubmed
  • De Giorgi J, Piskurewicz U, Loubery S, Utz-Pugin A, Bailly C, Mène-Saffrané L, Lopez-Molina L. An endosperm-associated cuticle is required for Arabidopsis seed viability, dormancy and early control of germination. PLoS Genet. 2015 Dec 17;11(12):e1005708. ► Pubmed
  • Di D, Sanchez-Mazas A, Currat M. Computer simulation of human leukocyte antigen genes supports two main routes of colonization by human populations in East Asia. BMC Evol Biol. 2015 Nov 4;15:240. ► Pubmed
  • Dieudonné FX, O’Connor PB, Gubler-Jaquier P, Yasrebi H, Conne B, Nikolaev S, Antonarakis S, Baranov PV, Curran J. The effect of heterogeneous Transcription Start Sites (TSS) on the translatome: implications for the mammalian cellular phenotype. BMC Genomics. 2015 Nov 21;16:986. ► Pubmed
  • Dos Santos Francisco R, Buhler S, Nunes JM, Bitarello BD, França GS, Meyer D, Sanchez-Mazas A. HLA supertype variation across populations: new insights into the role of natural selection in the evolution of HLA-A and HLA-B polymorphisms. Immunogenetics. 2015 Nov;67(11-12):651-63. ► Pubmed
  • Gaubitz C, Oliveira TM, Prouteau M, Leitner A, Karuppasamy M, Konstantinidou G, Rispal D, Eltschinger S, Robinson GC, Thore S, Aebersold R, Schaffitzel C, Loewith R. Molecular basis of the rapamycin insensitivity of Target Of Rapamycin Complex 2. Mol Cell. 2015 Jun 18;58(6):977-88. ► Pubmed
  • GTEx Consortium. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans. Science. 2015 May 8;348(6235):648-60. ► Pubmed
  • Guipponi M, Chentouf A, Webling KE, Freimann K, Crespel A, Nobile C, Lemke JR, Hansen J, Dorn T, Lesca G, Ryvlin P, Hirsch E, Rudolf G, Rosenberg DS, Weber Y, Becker F, Helbig I, Muhle H, Salzmann A, Chaouch M, Oubaiche ML, Ziglio S, Gehrig C, Santoni F, Pizzato M, Langel Ü, Antonarakis SE. Galanin pathogenic mutations in temporal lobe epilepsy. Hum Mol Genet. 2015 Jun 1;24(11):3082-91. ► Pubmed
  • Gutierrez-Arcelus M, Ongen H, Lappalainen T, Montgomery SB, Buil A, Yurovsky A, Bryois J, Padioleau I, Romano L, Planchon A, Falconnet E, Bielser D, Gagnebin M, Giger T, Borel C, Letourneau A, Makrythanasis P, Guipponi M, Gehrig C, Antonarakis SE, Dermitzakis ET. Tissue-specific effects of genetic and epigenetic variation on gene regulation and splicing. PLoS Genet. 2015 Jan 29;11(1):e1004958. ► Pubmed
  • Jacquier N, Frandi A, Viollier PH, Greub G. Disassembly of a medial transenvelope structure by antibiotics during intracellular division. Chem Biol. 2015 Sep 17;22(9):1217-27. ► Pubmed
  • Jacquier N, Viollier PH, Greub G. The role of peptidoglycan in chlamydial cell division: towards resolving the chlamydial anomaly. FEMS Microbiol Rev. 2015 Mar;39(2):262-75. ► Pubmed
  • Joshi KK, Bergé M, Radhakrishnan SK, Viollier PH, Chien P. An adaptor hierarchy regulates proteolysis during a bacterial cell cycle. Cell. 2015 Oct 8;163(2):419-31. ► Pubmed
  • Jourdain AA, Koppen M, Rodley CD, Maundrell K, Gueguen N, Reynier P, Guaras AM, Enriquez JA, Anderson P, Simarro M, Martinou JC. A mitochondria-specific isoform of FASTK is present in mitochondrial RNA granules and regulates gene expression and function. Cell Rep. 2015 Feb 24;10(7):1110-21. ► Pubmed
  • Kang J, Yim S, Choi H, Kim A, Lee KP, Lopez-Molina L, Martinoia E, Lee Y. Abscisic acid transporters cooperate to control seed germination. Nat Commun. 2015 Sep 3;6:8113. ► Pubmed
  • Korhonen HM, Yadav RP, Da Ros M, Chalmel F, Zimmermann C, Toppari J, Nef S, Kotaja N. DICER regulates the formation and maintenance of cell-cell junctions in the mouse seminiferous epithelium. Biol Reprod. 2015 Dec;93(6):139. ► Pubmed
  • Kourtidis A, Ngok SP, Pulimeno P, Feathers RW, Carpio LR, Baker TR, Carr JM, Yan IK, Borges S, Perez EA, Storz P, Copland JA, Patel T, Thompson EA, Citi S, Anastasiadis PZ. Distinct E-cadherin-based complexes regulate cell behaviour through miRNA processing or Src and p120 catenin activity. Nat Cell Biol. 2015 Sep;17(9):1145-57. ► Pubmed
  • Kubik S, Bruzzone MJ, Jacquet P, Falcone JL, Rougemont J, Shore D. Nucleosome stability distinguishes two different promoter types at all protein-coding genes in yeast. Mol Cell. 2015 Nov 5;60(3):422-34. ► Pubmed
  • Legrand N, Jaquier-Gubler P, Curran J. The impact of the phosphomimetic eIF2αS/D on global translation, reinitiation and the integrated stress response is attenuated in N2a cells. Nucleic Acids Res. 2015 Sep 30;43(17):8392-404. ► Pubmed
  • Letourneau A, Cobellis G, Fort A, Santoni F, Garieri M, Falconnet E, Ribaux P, Vannier A, Guipponi M, Carninci P, Borel C, Antonarakis SE. HSA21 Single-Minded 2 (Sim2) binding sites co-localize with super-enhancers and pioneer transcription factors in pluripotent mouse ES cells. PLoS One. 2015 May 8;10(5):e0126475. ► Pubmed
  • Longoni P, Douchi D, Cariti F, Fucile G, Goldschmidt-Clermont M. Phosphorylation of the Light-harvesting complex II isoform Lhcb2 is central to state transitions. Plant Physiol. 2015 Dec;169(4):2874-83. ► Pubmed
  • Lukowski SW, Fish RJ, Martin-Levilain J, Gonelle-Gispert C, Bühler LH, Maechler P, Dermitzakis ET, Neerman-Arbez M. Integrated analysis of mRNA and miRNA expression in response to interleukin-6 in hepatocytes. Genomics. 2015 Aug;106(2):107-15. ► Pubmed
  • Melé M, Ferreira PG, Reverter F, DeLuca DS, Monlong J, Sammeth M, Young TR, Goldmann JM, Pervouchine DD, Sullivan TJ, Johnson R, Segrè AV, Djebali S, Niarchou A, GTEx Consortium, Wright FA, Lappalainen T, Calvo M, Getz G, Dermitzakis ET, Ardlie KG, Guigó R. The human transcriptome across tissues and individuals. Science. 2015 May 8;348(6235):660-5. ► Pubmed
  • Ongen H, Dermitzakis ET. Alternative splicing QTLs in European and African populations. Am J Hum Genet. 2015 Oct 1;97(4):567-75. ► Pubmed
  • Panis G, Murray SR, Viollier PH. Versatility of global transcriptional regulators in alpha-Proteobacteria: from essential cell cycle control to ancillary functions. FEMS Microbiol Rev. 2015 Jan;39(1):120-33. ► Pubmed
  • Pini F, De Nisco NJ, Ferri L, Penterman J, Fioravanti A, Brilli M, Mengoni A, Bazzicalupo M, Viollier PH, Walker GC, Biondi EG. Cell cycle control by the master regulator CtrA in Sinorhizobium meliloti. PLoS Genet. 2015 May 15;11(5):e1005232. ► Pubmed
  • Quilodrán CS, Montoya-Burgos JI, Currat M. Modelling interspecific hybridization with genome exclusion to identify conservation actions: the case of native and invasive Pelophylax waterfrogs. Evol Appl. 2015 Feb;8(2):199-210. ► Pubmed
  • Rispal D, Eltschinger S, Stahl M, Vaga S, Bodenmiller B, Abraham Y, Filipuzzi I, Movva NR, Aebersold R, Helliwell SB, Loewith R. Target of rapamycin complex 2 regulates actin polarization and endocytosis via multiple pathways. J Biol Chem. 2015 Jun 12;290(24):14963-78. ► Pubmed
  • Rivas MA, Pirinen M, Conrad DF, Lek M, Tsang EK, Karczewski KJ, Maller JB, Kukurba KR, DeLuca DS, Fromer M, Ferreira PG, Smith KS, Zhang R, Zhao F, Banks E, Poplin R, Ruderfer DM, Purcell SM, Tukiainen T, Minikel EV, Stenson PD, Cooper DN, Huang KH, Sullivan TJ, Nedzel J, GTEx Consortium, Geuvadis Consortium, Bustamante CD, Li JB, Daly MJ, Guigo R, Donnelly P, Ardlie K, Sammeth M, Dermitzakis ET, McCarthy MI, Montgomery SB, Lappalainen T, MacArthur DG. Effect of predicted protein-truncating genetic variants on the human transcriptome. Science. 2015 May 8;348(6235):666-9. ► Pubmed
  • Rosa A, Chande A, Ziglio S, De Sanctis V, Bertorelli R, Goh SL, McCauley SM, Nowosielska A, Antonarakis SE, Luban J, Santoni FA, Pizzato M. HIV-1 Nef promotes infection by excluding SERINC5 from virion incorporation. Nature. 2015 Oct 8;526(7572):212-7. ► Pubmed
  • Sailani MR, Santoni FA, Letourneau A, Borel C, Makrythanasis P, Hibaoui Y, Popadin K, Bonilla X, Guipponi M, Gehrig C, Vannier A, Carre-Pigeon F, Feki A, Nizetic D, Antonarakis SE. DNA-methylation patterns in trisomy 21 using cells from monozygotic twins. PLoS One. 2015 Aug 28;10(8):e0135555. ► Pubmed
  • Sanselicio S, Bergé M, Théraulaz L, Radhakrishnan SK, Viollier PH. Topological control of the Caulobacter cell cycle circuitry by a polarized single-domain PAS protein. Nat Commun. 2015 May 8;6:7005. ► Pubmed
  • Sanselicio S, Viollier PH. Convergence of alarmone and cell cycle signaling from trans-encoded sensory domains. MBio. 2015 Oct 20;6(5). pii: e01415-15. ► Pubmed
  • Santoni FA, Makrythanasis P, Antonarakis SE. CATCHing putative causative variants in consanguineous families. BMC Bioinformatics. 2015 Sep 28;16:310. ► Pubmed
  • Texari L, Stutz F. Sumoylation and transcription regulation at nuclear pores. Chromosoma. 2015 Mar;124(1):45-56. ► Pubmed
  • Tille JC, Ho L, Shah J, Seyde O, McKee TA, Citi S. The expression of the zonula adhaerens protein PLEKHA7 is strongly decreased in high grade ductal and lobular breast carcinomas. PLoS One. 2015 Aug 13;10(8):e0135442. ► Pubmed
  • Tymoshenko S, Oppenheim RD, Agren R, Nielsen J, Soldati-Favre D, Hatzimanikatis V. Metabolic needs and capabilities of Toxoplasma gondii through combined computational and experimental analysis. PLoS Comput Biol. 2015 May 22;11(5):e1004261. ► Pubmed
  • Tzika AC, Ullate-Agote A, Grbic D, Milinkovitch MC. Reptilian Transcriptomes v2.0: an extensive resource for Sauropsida genomics and transcriptomics. Genome Biol Evol. 2015 Jul 1;7(6):1827-41. ► Pubmed
  • Villanyi Z, Collart MA. Ccr4-Not is at the core of the eukaryotic gene expression circuitry. Biochem Soc Trans. 2015 Dec;43(6):1253-8. ► Pubmed
  • Waszak SM, Delaneau O, Gschwind AR, Kilpinen H, Raghav SK, Witwicki RM, Orioli A, Wiederkehr M, Panousis NI, Yurovsky A, Romano-Palumbo L, Planchon A, Bielser D, Padioleau I, Udin G, Thurnheer S, Hacker D, Hernandez N, Reymond A, Deplancke B, Dermitzakis ET. Population variation and genetic control of modular chromatin architecture in humans. Cell. 2015 Aug 27;162(5):1039-50. ► Pubmed
  • Weiss B, Curran JA. CAP(+) selection: A combined chemical-enzymatic strategy for efficient eukaryotic messenger RNA enrichment via the 5′ cap. Anal Biochem. 2015 Sep 1;484:72-4. ► Pubmed

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