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Research articles

Publications including work performed in the frame of iGE3
2012 & 2013

Alphabetical order of first authors’ names

2013

  • Castelnuovo M, Rahman S, Guffanti E, Infantino V, Stutz F, Zenklusen D. Bimodal expression of PHO84 is modulated by early termination of antisense transcription. Nat Struct Mol Biol. 2013 Jul;20(7):851-8.  >>> Pubmed
  • Castelnuovo M, Stutz F. Gene loops and HDACs to promote transcription directionality. Nucleus. 2013 Mar-Apr;4(2):92-4.  >>> Pubmed
  • Collart MA. The NOT4 RING E3 ligase: a relevant player in cotranslational quality control. ISRN Mol Biol. 2013 Jan 21;2013:548359.  >>> Pubmed
  • Collart M, Panasenko O, Nikolaev S. The Not3/5 subunit of the Ccr4-Not complex: A central regulator of gene expression that integrates signals between the cytoplasm and the nucleus in eukaryotic cells. Cell Signal. 2013 Apr;25(4):743-51.  >>> Pubmed
  • C’t Hoen PA, Friedländer MR, Almlöf J, Sammeth M, Pulyakhina I, Anvar SY, Laros JF, Buermans HP, Karlberg O, Brännvall M; GEUVADIS Consortium, den Dunnen JT, van Ommen GJ, Gut IG, Guigó R, Estivill X, Syvänen AC, Dermitzakis ET, Lappalainen T. Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories. Nat Biotechnol. 2013 Nov;31(11):1015-22.  >>> Pubmed
  • Davis NJ, Cohen Y, Sanselicio S, Fumeaux C, Ozaki S, Luciano J, Guerrero-Ferreira RC, Wright ER, Jenal U, Viollier PH. De- and repolarization mechanism of flagellar morphogenesis during a bacterial cell cycle. Genes Dev. 2013 Sep 15;27(18):2049-62.  >>> Pubmed
  • De la Rossa A, Bellone C, Golding B, Vitali I, Moss J, Toni N, Lüscher C, Jabaudon D. In vivo reprogramming of circuit connectivity in postmitotic neocortical neurons. Nat Neurosci. 2013 Feb;16(2):193-200.  >>> Pubmed
  • Guillemot L, Spadaro D, Citi S. The junctional proteins cingulin and paracingulin modulate the expression of tight junction protein genes through GATA-4. PLoS ONE 2013 Feb;8(2):e55873.  >>> Pubmed
  • Gutierrez-Arcelus M, Lappalainen T, Montgomery SB, Buil A, Ongen H, Yurovsky A, Bryois J, Giger T, Romano L, Planchon A, Falconnet E, Bielser D, Gagnebin M, Padioleau I, Borel C, Letourneau A, Makrythanasis P, Guipponi M, Gehrig C, Antonarakis SE, Dermitzakis ET. Passive and active DNA methylation and the interplay with genetic variation in gene regulation. Elife. 2013 Jun 4;2:e00523.  >>> Pubmed
  • Jourdain AA, Koppen M, Wydro M, Rodley CD, Lightowlers RN, Chrzanowska-Lightowlers ZM, Martinou JC. GRSF1 regulates RNA processing in mitochondrial RNA granules. Cell Metab. 2013 Mar 5;17(3):399-410.  >>> Pubmed
  • Lappalainen T, Sammeth M, Friedländer MR, C’t Hoen PA, Monlong J, Rivas MA, Gonzàlez-Porta M, Kurbatova N, Griebel T, Ferreira PG, Barann M, Wieland T, Greger L, van Iterson M, Almlöf J, Ribeca P, Pulyakhina I, Esser D, Giger T, Tikhonov A, Sultan M, Bertier G, MacArthur DG, Lek M, Lizano E, Buermans HP, Padioleau I, Schwarzmayr T, Karlberg O, Ongen H, Kilpinen H, Beltran S, Gut M, Kahlem K, Amstislavskiy V, Stegle O, Pirinen M, Montgomery SB, Donnelly P, McCarthy MI, Flicek P, Strom TM; Geuvadis Consortium, Lehrach H, Schreiber S, Sudbrak R, Carracedo A, Antonarakis SE, Häsler R, Syvänen AC, van Ommen GJ, Brazma A, Meitinger T, Rosenstiel P, Guigó R, Gut IG, Estivill X, Dermitzakis ET; Geuvadis Consortium. Transcriptome and genome sequencing uncovers functional variation in humans. Nature. 2013 Sep 26;501(7468):506-11.  >>> Pubmed
  • Murray SM, Panis G, Fumeaux C, Viollier PH, Howard M. Computational and genetic reduction of a cell cycle to its simplest, primordial components. PLoS Biol. 2013 Dec;11(12):e1001749.  >>> Pubmed
  • Nica AC, Ongen H, Irminger JC, Bosco D, Berney T, Antonarakis SE, Halban PA, Dermitzakis ET. Cell-type, allelic, and genetic signatures in the human pancreatic beta cell transcriptome. Genome Res. 2013 Sep;23(9):1554-62.  >>> Pubmed
  • Nikolaev SI, Santoni F, Vannier A, Falconnet E, Giarin E, Basso G, Hoischen A, Veltman JA, Groet J, Nizetic D, Antonarakis SE. Exome sequencing identifies putative drivers of progression of transient myeloproliferative disorder to AMKL in infants with Down syndrome. Blood. 2013 Jul 25;122(4):554-61.  >>> Pubmed
  • Pitetti J-L, Calvel P, Romero Y, Conne B, Truong V, Papaioannou MD, Schaad O, Docquier M, Herrera PL, Wilhelm D, Nef S. Insulin and IGF1 receptors are essential for XX and XY gonadal differentiation and adrenal development in mice. PLoS Genet. 2013 Jan;9(1):e1003160.  >>> Pubmed
  • Popadin K, Gutierrez-Arcelus M, Dermitzakis ET, Antonarakis SE. Genetic and epigenetic regulation of human lincRNA gene expression. Am J Hum Genet. 2013 Dec 5;93(6):1015-26.  >>> Pubmed
  • Popadin KY, Nikolaev SI, Junier T, Baranova M, Antonarakis SE. Purifying selection in mammalian mitochondrial protein-coding genes is highly effective and congruent with evolution of nuclear genes. Mol Biol Evol. 2013 Feb;30(2): 347-355.  >>> Pubmed
  • Rihs TA, Tomescu MI, Britz J, Rochas V, Custo A, Schneider M, Debbané M, Eliez S, Michel CM. Altered auditory processing in frontal and left temporal cortex in 22q11.2 deletion syndrome: A group at high genetic risk for schizophrenia. Psychiatry Res. 2013 May 30;212(2):141-9.  >>> Pubmed
  • Sailani MR, Makrythanasis P, Valsesia A, Santoni FA, Deutsch S, Popadin K, Borel C, Migliavacca E, Sharp AJ, Duriaux Sail G, Falconnet E, Rabionet K, Serra-Juhé C, Vicari S, Laux D, Grattau Y, Dembour G, Megarbane A, Touraine R, Stora S, Kitsiou S, Fryssira H, Chatzisevastou-Loukidou C, Kanavakis E, Merla G, Bonnet D, Pérez-Jurado LA, Estivill X, Delabar JM, Antonarakis SE. The complex SNP and CNV genetic architecture of the increased risk of congenital heart defects in Down syndrome. Genome Res. 2013 Sep;23(9):1410-21.  >>> Pubmed
  • Sanchez-Mazas A, Buhler S, Nunes JM. A new HLA map of Europe: Regional genetic variation and its implication for peopling history, disease-association studies and tissue transplantation. Hum Hered. 2013;76(3-4):162-77.  >>> Pubmed
  • Shi T, Bunker RD, Mattarocci S, Ribeyre C, Faty M, Gut H, Scrima A, Rass U, Rubin SM, Shore D, Thomä NH. Rif1 and Rif2 shape telomere function and architecture through multivalent Rap1 interactions. Cell. 2013 Jun 6;153(6):1340-53.  >>> Pubmed
  • Steijger T, Abril JF, Engström PG, Kokocinski F; RGASP Consortium, Abril JF, Akerman M, Alioto T, Ambrosini G, Antonarakis SE, Behr J, Bertone P. Assessment of transcript reconstruction methods for RNA-seq. Nat Methods. 2013 Dec;10(12):1177-84.  >>> Pubmed
  • Texari L, Dieppois G, Vinciguerra P, Contreras MP, Groner A, Letourneau A, Stutz F. The nuclear pore regulates GAL1 gene transcription by controlling the localization of the SUMO protease Ulp1. Mol Cell. 2013 Sep 26;51(6):807-18.  >>> Pubmed
  • Vorjohann S, Pitetti JL, Nef S, Gonelle-Gispert C, Buhler L, Fish RJ, Neerman-Arbez M. DNA methylation profiling of the fibrinogen gene landscape in human cells and during mouse and zebrafish development. PLoS One. 2013 Aug 21;8(8):e73089.  >>> Pubmed
  • Wenger Y, Galliot B. Punctuated emergences of genetic and phenotypic innovations in eumetazoan, bilaterian, euteleostome, and hominidae ancestors. Genome Biol Evol. 2013 Jan;5(10):1949-68.  >>> Pubmed
  • Wenger Y, Galliot B. RNAseq versus genome-predicted transcriptomes: a large population of novel transcripts identified in an Illumina-454 Hydra transcriptome. BMC Genomics. 2013 Mar 25;14:204.  >>> Pubmed

2012

  • Andrés-Barrao C, Saad MM, Chappuis ML, Boffa M, Perret X, Ortega Pérez R, Barja F. Proteome analysis of Acetobacter pasteurianus during acetic acid fermentation. J Proteomics. 2012 Mar 16;75(6):1701-17.  >>> Pubmed
  • Borel C, Migliavacca E, Letourneau A, Gagnebin M, Béna F, Sailani MR, Dermitzakis ET, Sharp AJ, Antonarakis SE. Tandem repeat sequence variation as causative cis-eQTLs for protein-coding gene expression variation: the case of CSTB. Hum Mutat. 2012 Aug;33(8):1302-9.  >>> Pubmed
  • Debbané M, Lazouret M, Lagioia A, Schneider M, Van De Ville D, Eliez S. Resting-state networks in adolescents with 22q11.2 deletion syndrome: associations with prodromal symptoms and executive functions. Schizophr Res. 2012 Aug;139(1-3):33-9.  >>> Pubmed
  • Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, Xue C, Marinov GK, Khatun J, Williams BA, Zaleski C, Rozowsky J, Röder M, Kokocinski F, Abdelhamid RF, Alioto T, Antoshechkin I, Baer MT, Bar NS, Batut P, Bell K, Bell I, Chakrabortty S, Chen X, Chrast J, Curado J, Derrien T, Drenkow J, Dumais E, Dumais J, Duttagupta R, Falconnet E, Fastuca M, Fejes-Toth K, Ferreira P, Foissac S, Fullwood MJ, Gao H, Gonzalez D, Gordon A, Gunawardena H, Howald C, Jha S, Johnson R, Kapranov P, King B, Kingswood C, Luo OJ, Park E, Persaud K, Preall JB, Ribeca P, Risk B, Robyr D, Sammeth M, Schaffer L, See LH, Shahab A, Skancke J, Suzuki AM, Takahashi H, Tilgner H, Trout D, Walters N, Wang H, Wrobel J, Yu Y, Ruan X, Hayashizaki Y, Harrow J, Gerstein M, Hubbard T, Reymond A, Antonarakis SE, Hannon G, Giddings MC, Ruan Y, Wold B, Carninci P, Guigó R, Gingeras TR. Landscape of transcription in human cells. Nature. 2012 Sep 6;489(7414):101-8.  >>> Pubmed
  • Fabbro A, Rizzi E, Schneider M, Debbane M, Eliez S. Depression and anxiety disorders in children and adolescents with velo-cardio-facial syndrome (VCFS). Eur Child Adolesc Psychiatry. 2012 Jul;21(7):379-85.  >>> Pubmed
  • Flahault A, Schaer M, Ottet MC, Debbané M, Eliez S. Hippocampal volume reduction in chromosome 22q11.2 deletion syndrome (22q11.2DS): a longitudinal study of morphometry and symptomatology. Psychiatry Res. 2012 Jul 30;203(1):1-5.  >>> Pubmed
  • Letourneau A, Antonarakis SE. Genomic determinants in the phenotypic variability of Down syndrome. Prog Brain Res. 2012;197:15-28.  >>> Pubmed
  • Nikolaev SI, Sotiriou SK, Pateras IS, Santoni F, Sougioultzis S, Edgren H, Almusa H, Robyr D, Guipponi M, Saarela J, Gorgoulis VG, Antonarakis SE, Halazonetis TD. A single-nucleotide substitution mutator phenotype revealed by exome sequencing of human colon adenomas. Cancer Res. 2012 Dec 1;72(23):6279-6289.  >>> Pubmed
  • Peduzzi S, Storelli N, Welsh A, Peduzzi R, Hahn D, Perret X, Tonolla M. Candidatus “Thiodictyon syntrophicum”, sp. nov., a new purple sulfur bacterium isolated from the chemocline of Lake Cadagno forming aggregates and specific associations with Desulfocapsa sp. Syst Appl Microbiol. 2012 May;35(3):139-44.  >>> Pubmed
  • Rahim G, Araud T, Jaquier-Gubler P, Curran J. Alternative splicing within the elk-1 5′ untranslated region serves to modulate initiation events downstream of the highly conserved upstream open reading frame 2. Mol Cell Biol. 2012 May;32(9):1745-56.  >>> Pubmed
  • Saad MM, Crèvecoeur M, Masson-Boivin C, Perret X. The type 3 protein secretion system of Cupriavidus taiwanensis strain LMG19424 compromises symbiosis with Leucaena leucocephala. Appl Environ Microbiol. 2012 Oct;78(20):7476-9.  >>> Pubmed
  • Schneider M, Debbané M, Lagioia A, Salomon R, d’Argembeau A, Eliez S. Comparing the neural bases of self-referential processing in typically developing and 22q11.2 adolescents. Dev Cogn Neurosci. 2012 Apr;2(2):277-89.  >>> Pubmed
  • Schneider M, Van der Linden M, Glaser B, Rizzi E, Dahoun SP, Hinard C, Bartoloni L, Antonarakis SE, Debbané M, Eliez S. Preliminary structure and predictive value of attenuated negative symptoms in 22q11.2 deletion syndrome. Psychiatry Res. 2012 Apr 30;196(2-3):277-84.  >>> Pubmed
  • Ziegler D, Mariotti A, Pflüger V, Saad M, Vogel G, Tonolla M, Perret X. In situ identification of plant-invasive bacteria with MALDI-TOF mass spectrometry. PLoS One. 2012;7(5):e37189.  >>> Pubmed
 
Latest modification: March 27, 2017 - 11 h 06

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