Publications including work performed in the frame of iGE3.
Alphabetical order of first authors' names

2018

  • Buhler S, Nunes JM, Sanchez-Mazas A. Correction to: HLA class I molecular variation and peptide-binding properties suggest a model of joint divergent asymmetric selection. Immunogenetics. 2018 Feb;70(2):141. Pubmed
  • Buzgariu W, Wenger Y, Tcaciuc N, Catunda-Lemos AP, Galliot B. Impact of cycling cells and cell cycle regulation on Hydra regeneration. Dev Biol. 2018 Jan 15;433(2):240-253. Pubmed
  • Černý V, Kulichová I, Poloni ES, Nunes JM, Pereira L, Mayor A, Sanchez-Mazas A. Genetic history of the African Sahelian populations. HLA. 2018 Mar;91(3):153-166. Pubmed
  • Citi S. Intestinal barriers protect against disease. Science. 2018 Mar 9;359(6380):1097-1098. Pubmed
  • Demarsy E, Goldschmidt-Clermont M, Ulm R. Coping with 'dark sides of the sun' through photoreceptor signaling. Trends Plant Sci. 2018 Mar;23(3):260-271. Pubmed
  • Dibner C, Schibler U. Body clocks: Time for the Nobel Prize. Acta Physiol (Oxf). 2018 Feb;222(2). Pubmed
  • Gabay C, Fautrel B, Rech J, Spertini F, Feist E, Kötter I, Hachulla E, Morel J, Schaeverbeke T, Hamidou MA, Martin T, Hellmich B, Lamprecht P, Schulze-Koops H, Courvoisier DS, Sleight A, Schiffrin EJ. Open-label, multicentre, dose-escalating phase II clinical trial on the safety and efficacy of tadekinig alfa (IL-18BP) in adult-onset Still's disease. Ann Rheum Dis. 2018 Feb 22. [Epub ahead of print]. Pubmed
  • Goeury T, Creary LE, Fernandez-Vina MA, Tiercy JM, Nunes JM, Sanchez-Mazas A. Mandenka from Senegal: Next Generation Sequencing typings reveal very high frequencies of particular HLA class II alleles and haplotypes. HLA. 2018 Feb;91(2):148-150. Pubmed
  • Hurst SA, Zellweger U, Bosshard G, Bopp M; Swiss Medical End-of-Life Decisions Study Group. Medical end-of-life practices in Swiss cultural regions: a death certificate study. BMC Med. 2018 Apr 20;16(1):54. 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
  • Nikolaev SI, Vetiska S, Bonilla X, Boudreau E, Jauhiainen S, Rezai Jahromi B, Khyzha N, DiStefano PV, Suutarinen S, Kiehl TR, Mendes Pereira V, Herman AM, Krings T, Andrade-Barazarte H, Tung T, Valiante T, Zadeh G, Tymianski M, Rauramaa T, Ylä-Herttuala S, Wythe JD, Antonarakis SE, Frösen J, Fish JE, Radovanovic I. Somatic activating KRAS mutations in arteriovenous malformations of the brain. N Engl J Med. 2018 Jan 18;378(3):250-261. Pubmed
  • Niquille M, Limoni G, Markopoulos F, Cadilhac C, Prados J, Holtmaat A, Dayer A. Neurogliaform cortical interneurons derive from cells in the preoptic area. Elife. 2018 Mar 20;7. pii: e32017. Pubmed
  • Nussberger B, Currat M, Quilodran CS, Ponta N, Keller LF. Range expansion as an explanation for introgression in European wildcats. Biological Conservation, Volume 218, February 2018, Pages 49-5. ScienceDirect
  • Petrenko V, Dibner C. Cell-specific resetting of mouse islet cellular clocks by glucagon, glucagon-like peptide 1 and somatostatin. Acta Physiol (Oxf). 2018 Apr;222(4):e13021. Pubmed
  • Popadin K, Peischl S, Garieri M, Sailani MR, Letourneau A, Santoni F, Lukowski SW, Bazykin GA, Nikolaev S, Meyer D, Excoffier L, Reymond A, Antonarakis SE. Slightly deleterious genomic variants and transcriptome perturbations in Down syndrome embryonic selection. Genome Res. 2018 Jan;28(1):1-10. doi: 10.1101/gr.228411.117. Pubmed
  • Quilodrán CS, Austerlitz F, Currat M, Montoya-Burgos JI. Cryptic biological invasions: a general model of hybridization. Sci Rep. 2018 Feb 5;8(1):2414. Pubmed
  • Stévant I, Nef S. Single cell transcriptome sequencing: A new approach for the study of mammalian sex determination. Mol Cell Endocrinol. 2018 Jan 26. [Epub ahead of print]. 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
  • Tas D, Stickley L, Miozzo F, Koch R, Loncle N, Sabado V, Gnägi B, Nagoshi E. Parallel roles of transcription factors dFOXO and FER2 in the development and maintenance of dopaminergic neurons. PLoS Genet. 2018 Mar 12;14(3):e1007271. Pubmed
  • Viñuela A, Brown AA, Buil A, Tsai PC, Davies MN, Bell JT, Dermitzakis ET, Spector TD, Small KS. Age-dependent changes in mean and variance of gene expression across tissues in a twin cohort. Hum Mol Genet. 2018 Feb 15;27(4):732-741. Pubmed

2017

  • Ansar M, Riazuddin S, Sarwar MT, Makrythanasis P, Paracha SA, Iqbal Z, Khan J, Assir MZ, Hussain M, Razzaq A, Polla DL, Taj AS, Holmgren A, Batool N, Misceo D, Iwaszkiewicz J, de Brouwer APM, Guipponi M, Hanquinet S, Zoete V, Santoni FA, Frengen E, Ahmed J, Riazuddin S, van Bokhoven H, Antonarakis SE. Biallelic variants in LINGO1 are associated with autosomal recessive intellectual disability, microcephaly, speech and motor delay. Genet Med. 2017 Aug 24. [Epub ahead of print]. Pubmed
  • 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
  • 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
  • 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
  • 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. Journal
  • 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

2016

  • Albert B, Knight B, Merwin J, Martin V, Ottoz D, Gloor Y, Bruzzone MJ, Rudner A, Shore D. A molecular titration system coordinates ribosomal protein gene transcription with ribosomal RNA synthesis. Mol Cell. 2016 Nov 17;64(4):720-733. Pubmed
  • Ardissone S, Redder P, Russo G, Frandi A, Fumeaux C, Patrignani A, Schlapbach R, Falquet L, Viollier PH. Cell cycle constraints and environmental control of local DNA hypomethylation in α-proteobacteria. PLoS Genet. 2016 Dec 20;12(12):e1006499. Pubmed
  • Bergé M, Campagne S, Mignolet J, Holden S, Théraulaz L, Manley S, Allain FH, Viollier PH. Modularity and determinants of a (bi-)polarization control system from free-living and obligate intracellular bacteria. Elife. 2016 Dec 23;5. pii: e20640. Pubmed
  • Binkert M, Crocco CD, Ekundayo B, Lau K, Raffelberg S, Tilbrook K, Yin R, Chappuis R, Schalch T, Ulm R. Revisiting chromatin binding of the Arabidopsis UV-B photoreceptor UVR8. BMC Plant Biol. 2016 Feb 11;16(1):42. Pubmed
  • Bonilla X, Parmentier L, King B, Bezrukov F, Kaya G, Zoete V, Seplyarskiy VB, Sharpe HJ, McKee T, Letourneau A, Ribaux PG, Popadin K, Basset-Seguin N, Chaabene RB, Santoni FA, Andrianova MA, Guipponi M, Garieri M, Verdan C, Grosdemange K, Sumara O, Eilers M, Aifantis I, Michielin O, de Sauvage FJ, Antonarakis SE, Nikolaev SI. Genomic analysis identifies new drivers and progression pathways in skin basal cell carcinoma. Nat Genet. 2016 Apr;48(4):398-406. Pubmed
  • Buhler S, Nunes JM, Sanchez-Mazas A. HLA class I molecular variation and peptide-binding properties suggest a model of joint divergent asymmetric selection. Immunogenetics. 2016 Jul;68(6-7):401-16. 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
  • Chera S, Herrera PL. Regeneration of pancreatic insulin-producing cells by in situ adaptive cell conversion. Curr Opin Genet Dev. 2016 Oct;40:1-10. Pubmed
  • Cigliola V, Thorel F, Chera S, Herrera PL. Stress-induced adaptive islet cell identity changes. Diabetes Obes Metab. 2016 Sep;18 Suppl 1:87-96. Pubmed
  • Collart MA. The Ccr4-Not complex is a key regulator of eukaryotic gene expression. Wiley Interdiscip Rev RNA. 2016 Jul;7(4):438-54. Pubmed
  • de Barsy M, Frandi A, Panis G, Théraulaz L, Pillonel T, Greub G, Viollier PH. Regulatory (pan-)genome of an obligate intracellular pathogen in the PVC superphylum. ISME J. 2016 Sep;10(9):2129-44. Pubmed
  • Denay G, Chahtane H, Tichtinsky G, Parcy F. A flower is born: an update on Arabidopsis floral meristem formation. Curr Opin Plant Biol. 2016 Oct 6;35:15-22. Pubmed
  • Eltschinger S, Loewith R. TOR complexes and the maintenance of cellular homeostasis. Trends Cell Biol. 2016 Feb;26(2):148-59. Pubmed
  • Fabbiano S, Suárez-Zamorano N, Rigo D, Veyrat-Durebex C, Stevanovic Dokic A, Colin DJ, Trajkovski M. Caloric restriction leads to browning of white adipose tissue through type 2 immune signaling. Cell Metab. 2016 Sep 13;24(3):434-46. Pubmed
  • Ferreira PG, Oti M, Barann M, Wieland T, Ezquina S, Friedländer MR, Rivas MA, Esteve-Codina A; GEUVADIS Consortium, Rosenstiel P, Strom TM, Lappalainen T, Guigó R, Sammeth M. Sequence variation between 462 human individuals fine-tunes functional sites of RNA processing. Sci Rep. 2016 Sep 12;6:32406. Pubmed
  • Fokstuen S, Makrythanasis P, Hammar E, Guipponi M, Ranza E, Varvagiannis K, Santoni FA, Albarca-Aguilera M, Poleggi ME, Couchepin F, Brockmann C, Mauron A, Hurst SA, Moret C, Gehrig C, Vannier A, Bevillard J, Araud T, Gimelli S, Stathaki E, Paoloni-Giacobino A, Bottani A, Sloan-Béna F, Sizonenko LD, Mostafavi M, Hamamy H, Nouspikel T, Blouin JL, Antonarakis SE. Experience of a multidisciplinary task force with exome sequencing for Mendelian disorders. Hum Genomics. 2016 Jun 28;10(1):24. Pubmed
  • Gaubitz C, Prouteau M, Kusmider B, Loewith R. TORC2 structure and function. Trends Biochem Sci. 2016 Jun;41(6):532-45. Pubmed
  • Glastonbury CA, Viñuela A, Buil A, Halldorsson GH, Thorleifsson G, Helgason H, Thorsteinsdottir U, Stefansson K, Dermitzakis ET, Spector TD, Small KS. Adiposity-dependent regulatory effects on multi-tissue transcriptomes. Am J Hum Genet. 2016 Sep 1;99(3):567-79. Pubmed
  • Guerrera D, Shah J, Vasileva E, Sluysmans S, Méan I, Jond L, Poser I, Mann M, Hyman AA, Citi S. PLEKHA7 recruits PDZD11 to adherens junctions to stabilize nectins. J Biol Chem. 2016 May 20;291(21):11016-29. Pubmed
  • Gupta I, Villanyi Z, Kassem S, Hughes C, Panasenko OO, Steinmetz LM, Collart MA. Translational capacity of a cell is determined during transcription elongation via the Ccr4-Not complex. Cell Rep. 2016 May 24;15(8):1782-94. Pubmed
  • Henrichfreise B, Brunke M, Viollier PH. Bacterial surfaces: the wall that SEDS built. Curr Biol. 2016 Nov 7;26(21):R1158-R1160. Pubmed
  • Janakiraman B, Mignolet J, Narayanan S, Viollier PH, Radhakrishnan SK. In-phase oscillation of global regulons is orchestrated by a pole-specific organizer. Proc Natl Acad Sci U S A. 2016 Nov 1;113(44):12550-12555. Pubmed
  • Job G, Brugger C, Xu T, Lowe BR, Pfister Y, Qu C, Shanker S, Baños Sanz JI, Partridge JF, Schalch T. SHREC silences heterochromatin via distinct remodeling and deacetylation modules. Mol Cell. 2016 Apr 21;62(2):207-21. Pubmed
  • Kirkpatrick CL, Martins D, Redder P, Frandi A, Mignolet J, Chapalay JB, Chambon M, Turcatti G, Viollier PH. Growth control switch by a DNA-damage-inducible toxin–antitoxin system in Caulobacter crescentus. Nat Microbiol. 2016 Feb 22;1:16008. Pubmed
  • Klöckner A, Bühl H, Viollier P, Henrichfreise B. Deconstructing the chlamydial cell wall. In ‘Current Topics in Microbiology and Immunology’, Springer, Berlin, Heidelberg, 2016: 1-33. Pubmed
  • Ligeiro D, Buhler S, Abecasis M, Abade O, Sanchez-Mazas A, da Silva MG, Trindade H. KIR genotypic diversity in Portuguese and analysis of KIR gene allocation after allogeneic hematopoietic stem cell transplantation. HLA. 2016 May;87(5):375-80. Pubmed
  • Lugli N, Kamileri I, Keogh A, Malinka T, Sarris ME, Talianidis I, Schaad O, Candinas D, Stroka D, Halazonetis TD. R-spondin 1 and noggin facilitate expansion of resident stem cells from non-damaged gallbladders. EMBO Rep. 2016 May;17(5):769-79. Pubmed
  • Makhlouf AM, Chitikova Z, Pusztaszeri M, Berczy M, Delucinge-Vivier C, Triponez F, Meyer P, Philippe J, Dibner C. Identification of CHEK1, SLC26A4, c-KIT, TPO and TG as new biomarkers for human follicular thyroid carcinoma. Oncotarget. 2016 Jul 19;7(29):45776-45788. Pubmed
  • Makrythanasis P, Guipponi M, Santoni FA, Zaki M, Issa MY, Ansar M, Hamamy H, Antonarakis SE. Exome sequencing discloses KALRN homozygous variant as likely cause of intellectual disability and short stature in a consanguineous pedigree. Hum Genomics. 2016 Jul 16;10(1):26. Pubmed
  • Mignolet J, Holden S, Bergé M, Panis G, Eroglu E, Théraulaz L, Manley S, Viollier PH. Functional dichotomy and distinct nanoscale assemblies of a cell cycle-controlled bipolar zinc-finger regulator. Elife. 2016 Dec 23;5. pii: e18647. Pubmed
  • Nicastro N, Ranza E, Antonarakis SE, Horvath J. Pure Progressive Ataxia and Palatal Tremor (PAPT) associated with a new Polymerase Gamma (POLG) mutation. Cerebellum. 2016 Dec;15(6):829-831. Pubmed
  • Ongen H, Buil A, Brown AA, Dermitzakis ET, Delaneau O. Fast and efficient QTL mapper for thousands of molecular phenotypes. Bioinformatics. 2016 May 15;32(10):1479-85. Pubmed
  • Petrenko V, Saini C, Perrin L, Dibner C. Parallel measurement of circadian clock gene expression and hormone secretion in human primary cell cultures. J Vis Exp. 2016 Nov 11;(117). Pubmed
  • Piskurewicz U, Iwasaki M, Susaki D, Megies C, Kinoshita T, Lopez-Molina L. Dormancy-specific imprinting underlies maternal inheritance of seed dormancy in Arabidopsis thaliana. Elife. 2016 Dec 22;5. pii: e19573. Pubmed
  • Rivera-Rivera CJ, Montoya-Burgos JI. LS3: a method for improving phylogenomic inferences when evolutionary rates are heterogeneous among taxa. Mol Biol Evol. 2016 Jun;33(6):1625-34. Pubmed
  • Romòn I, Montes C, Ligeiro D, Trindade H, Sanchez-Mazas A, Nunes JM, Buhler S. Mapping the HLA diversity of the Iberian Peninsula. Hum Immunol. 2016 Oct;77(10):832-40. Pubmed
  • Saini C, Petrenko V, Pulimeno P, Giovannoni L, Berney T, Hebrok M, Howald C, Dermitzakis ET, Dibner C. A functional circadian clock is required for proper insulin secretion by human pancreatic islet cells. Diabetes Obes Metab. 2016 Apr;18(4):355-65. Pubmed
  • Schossleitner K, Rauscher S, Gröger M, Friedl HP, Finsterwalder R, Habertheuer A, Sibilia M, Brostjan C, Födinger D, Citi S, Petzelbauer P. Evidence that cingulin regulates endothelial barrier function in vitro and in vivo. Arterioscler Thromb Vasc Biol. 2016 Apr;36(4):647-54. Pubmed
  • Shah J, Guerrera D, Vasileva E, Sluysmans S, Bertels E, Citi S. PLEKHA7: Cytoskeletal adaptor protein at center stage in junctional organization and signaling. Int J Biochem Cell Biol. 2016 Jun;75:112-6. Pubmed
  • Shyian M, Mattarocci S, Albert B, Hafner L, Lezaja A, Costanzo M, Boone C, Shore D. Budding yeast Rif1 controls genome integrity by inhibiting rDNA replication. PLoS Genet. 2016 Nov 7;12(11):e1006414. Pubmed
  • Styles EB, Founk KJ, Zamparo LA, Sing TL, Altintas D, Ribeyre C, Ribaud V, Rougemont J, Mayhew D, Costanzo M, Usaj M, Verster AJ, Koch EN, Novarina D, Graf M, Luke B, Muzi-Falconi M, Myers CL, Mitra RD, Shore D, Brown GW, Zhang Z, Boone C1, Andrews BJ. Exploring quantitative yeast phenomics with single-cell analysis of DNA damage foci. Cell Syst. 2016 Sep 28;3(3):264-277.e10. Pubmed
  • Telley L, Govindan S, Prados J, Stevant I, Nef S, Dermitzakis E, Dayer A, Jabaudon D. Sequential transcriptional waves direct the differentiation of newborn neurons in the mouse neocortex. Science. 2016 Mar 25;351(6280):1443-6. Pubmed
  • Tilbrook K, Dubois M, Crocco CD, Yin R, Chappuis R, Allorent G, Schmid-Siegert E, Goldschmidt-Clermont M, Ulm R. UV-B perception and acclimation in Chlamydomonas reinhardtii. Plant Cell. 2016 Apr;28(4):966-83. Pubmed
  • Trajkovski M, Wollheim CB. Physiology: Microbial signals to the brain control weight. Nature. 2016 Jun 8;534(7606):185-7. Pubmed
  • Villanyi Z, Collart MA. Building on the Ccr4-Not architecture. Bioessays. 2016 Oct;38(10):997-1002. Pubmed
  • Vogg MC, Wenger Y, Galliot B. How somatic adult tissues develop organizer activity. Curr Top Dev Biol. 2016;116:391-414. Pubmed
  • Wenger Y, Buzgariu W, Galliot B. Loss of neurogenesis in Hydra leads to compensatory regulation of neurogenic and neurotransmission genes in epithelial cells. Philos Trans R Soc Lond B Biol Sci. 2016 Jan 5;371(1685):20150040. Pubmed

2015

  • Ardissone S, Viollier PH. Interplay between flagellation and cell cycle control in Caulobacter. Curr Opin Microbiol. 2015 Oct 15;28:83-92. 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
  • 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
  • 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

2014

  • Ardissone S, Fumeaux C, Bergé M, Beaussart A, Théraulaz L, Radhakrishnan SK, Dufrêne YF, Viollier PH. Cell cycle constraints on capsulation and bacteriophage susceptibility. eLife 2014 Nov 25;3:e03587. Pubmed
  • Bryois J, Buil A, Evans DM, Kemp JP, Montgomery SB, Conrad DF, Ho KM, Ring S, Hurles M, Deloukas P, Davey Smith G, Dermitzakis ET. Cis and trans effects of human genomic variants on gene expression. PLoS Genet. 2014 Jul 10;10(7):e1004461. Pubmed
  • Callier P, Calvel P, Matevossian A, Makrythanasis P, Bernard P, Kurosaka H, Vannier A, Thauvin-Robinet C, Borel C, Mazaud-Guittot S, Rolland A, Desdoits-Lethimonier C, Guipponi M, Zimmermann C, Stévant I, Kuhne F, Conne B, Santoni F, Lambert S, Huet F, Mugneret F, Jaruzelska J, Faivre L, Wilhelm D, Jégou B, Trainor PA, Resh MD, Antonarakis SE, Nef S. Loss of function mutation in the palmitoyl-transferase HHAT leads to syndromic 46,XY disorder of sex development by impeding Hedgehog protein palmitoylation and signaling. PLoS Genet. 2014 May 1;10(5):e1004340. Pubmed
  • Castelnuovo M, Zaugg JB, Guffanti E, Maffioletti A, Camblong J, Xu Z, Clauder-Münster S, Steinmetz LM, Luscombe NM, Stutz F. Role of histone modifications and early termination in pervasive transcription and antisense-mediated gene silencing in yeast. Nucleic Acids Res. 2014 Apr;42(7):4348-62. Pubmed
  • Collart MA, Reese JC. Gene expression as a circular process: Cross-talk between transcription and mRNA degradation in eukaryotes. RNA Biol. 2014 Apr 1;11(4):320-3. Pubmed
  • Excoffier L, Quilodran CS, Currat M. Models of hybridization during range expansions and their application to recent human evolution. In ‘Cultural Developments in the Eurasian Paleolithic and the Origin of Anatomically Modern Humans’, edited by Derevianko AP & Shunkov M, Department of the Institute of Archaeology and Ethnography SB RAS, Novosibirsk, Russia, 2014: 122-137. Access to full text
  • Feaga HA, Viollier PH, Keiler KC. Release of nonstop ribosomes is essential. MBio. 2014 Nov 11;5(6). pii: e01916-14. Pubmed
  • Fiebig A, Herrou J, Fumeaux C, Radhakrishnan SK, Viollier PH, Crosson S. A cell cycle and nutritional checkpoint controlling bacterial surface adhesion. PLoS Genet. 2014 Jan;10(1):e1004101. Pubmed
  • Fish RJ, Di Sanza C, Neerman-Arbez M. Targeted mutation of zebrafish fga models human congenital afibrinogenemia. Blood. 2014 Apr 3;123(14):2278-81. Pubmed
  • Frandi A, Jacquier N, Théraulaz L, Greub G, Viollier PH. FtsZ-independent septal recruitment and function of cell wall remodelling enzymes in chlamydial pathogens. Nat Commun. 2014 Jun 23;5:4200. Pubmed
  • Fumeaux C, Radhakrishnan SK, Ardissone S, Théraulaz L, Frandi A, Martins D, Nesper J, Abel S, Jenal U, Viollier PH. Cell cycle transition from S-phase to G1 in Caulobacter is mediated by ancestral virulence regulators. Nat Commun. 2014 Jun 18;5:4081. Pubmed
  • Gannagé-Yared MH, Makrythanasis P, Chouery E, Sobacchi C, Mehawej C, Santoni FA, Guipponi M, Antonarakis SE, Hamamy H, Mégarbané A. Exome sequencing reveals a mutation in DMP1 in a family with familial sclerosing bone dysplasia. Bone. 2014 Nov;68:142-5. Pubmed
  • Griffeth RJ, Bianda V, Nef S. The emerging role of insulin-like growth factors in testis development and function. Basic Clin Androl. 2014 Aug 18;24:12. Pubmed
  • Guipponi M, Santoni FA, Setola V, Gehrig C, Rotharmel M, Cuenca M, Guillin O, Dikeos D, Georgantopoulos G, Papadimitriou G, Curtis L, Méary A, Schürhoff F, Jamain S, Avramopoulos D, Leboyer M, Rujescu D, Pulver A, Campion D, Siderovski DP, Antonarakis SE. Exome sequencing in 53 sporadic cases of schizophrenia identifies 18 putative candidate genes. PLoS One. 2014 Nov 24;9(11):e112745. Pubmed
  • Halter D, Collart MA, Panasenko OO. The Not4 E3 ligase and CCR4 deadenylase play distinct roles in protein quality control. PLoS One. 2014 Jan 17;9(1):e86218. Pubmed
  • Hibaoui Y, Grad I, Letourneau A, Sailani MR, Dahoun S, Santoni FA, Gimelli S, Guipponi M, Pelte MF, Béna F, Antonarakis SE, Feki A. Modelling and rescuing neurodevelopmental defect of Down syndrome using induced pluripotent stem cells from monozygotic twins discordant for trisomy 21. EMBO Mol Med. 2014 Feb;6(2):259-77. Pubmed
  • Hibaoui Y, Grad I, Letourneau A, Santoni FA, Antonarakis SE, Feki A. Data in brief: Transcriptome analysis of induced pluripotent stem cells from monozygotic twins discordant for trisomy 21. Genom Data. 2014 Aug 1;2:226-9. Pubmed
  • Jacquier N, Frandi A, Pillonel T, Viollier P, Greub G. Cell wall precursors are required to organize the chlamydial division septum. Nat Commun. 2014 Apr 8;5:3578. Pubmed
  • Kirkpatrick CL, Viollier PH. Synthetic interaction between the TipN polarity factor and an AcrAB-family efflux pump implicates cell polarity in bacterial drug resistance. Chem Biol. 2014 May 22;21(5):657-65. Pubmed
  • Knight B, Kubik S, Ghosh B, Bruzzone MJ, Geertz M, Martin V, Dénervaud N, Jacquet P, Ozkan B, Rougemont J, Maerkl SJ, Naef F, Shore D. Two distinct promoter architectures centered on dynamic nucleosomes control ribosomal protein gene transcription. Genes Dev. 2014 Aug 1;28(15):1695-709. Pubmed
  • Legrand N, Araud T, Conne B, Kuijpers O, Jaquier-Gubler P, Curran J. An AUG codon conserved for protein function rather than translational initiation: the story of the protein sElk1. PLoS One. 2014 Jul 18;9(7):e102890. Pubmed
  • Letourneau A, Santoni FA, Bonilla X, Sailani MR, Gonzalez D, Kind J, Chevalier C, Thurman R, Sandstrom RS, Hibaoui Y, Garieri M, Popadin K, Falconnet E, Gagnebin M, Gehrig C, Vannier A, Guipponi M, Farinelli L, Robyr D, Migliavacca E, Borel C, Deutsch S, Feki A, Stamatoyannopoulos JA, Herault Y, van Steensel B, Guigo R, Antonarakis SE. Domains of genome-wide gene expression dysregulation in Down’s syndrome. Nature. 2014 Apr 17;508(7496):345-50. Pubmed
  • MacArthur DG, Manolio TA, Dimmock DP, Rehm HL, Shendure J, Abecasis GR, Adams DR, Altman RB, Antonarakis SE, Ashley EA, Barrett JC, Biesecker LG, Conrad DF, Cooper GM, Cox NJ, Daly MJ, Gerstein MB, Goldstein DB, Hirschhorn JN, Leal SM, Pennacchio LA, Stamatoyannopoulos JA, Sunyaev SR, Valle D, Voight BF, Winckler W, Gunter C. Guidelines for investigating causality of sequence variants in human disease. Nature. 2014 Apr 24;508(7497):469-76. Pubmed
  • Nikolaev SI, Garieri M, Santoni F, Falconnet E, Ribaux P, Guipponi M, Murray A, Groet J, Giarin E, Basso G, Nizetic D, Antonarakis SE. Frequent cases of RAS-mutated Down syndrome acute lymphoblastic leukaemia lack JAK2 mutations. Nat Commun. 2014 Aug 8;5:4654. Pubmed
  • Nikolaev S, Santoni F, Garieri M, Makrythanasis P, Falconnet E, Guipponi M, Vannier A, Radovanovic I, Bena F, Forestier F, Schaller K, Dutoit V, Clement-Schatlo V, Dietrich PY, Antonarakis SE. Extrachromosomal driver mutations in glioblastoma and low-grade glioma. Nat Commun. 2014 Dec 4;5:5690. Pubmed
  • Nunes JM, Buhler S, Roessli D, Sanchez-Mazas A; HLA-net 2013 collaboration. The HLA-net GENE[RATE] pipeline for effective HLA data analysis and its application to 145 population samples from Europe and neighbouring areas. Tissue Antigens. 2014 May;83(5):307-23. Pubmed
  • Ongen H, Andersen CL, Bramsen JB, Oster B, Rasmussen MH, Ferreira PG, Sandoval J, Vidal E, Whiffin N, Planchon A, Padioleau I, Bielser D, Romano L, Tomlinson I, Houlston RS, Esteller M, Orntoft TF, Dermitzakis ET. Putative cis-regulatory drivers in colorectal cancer. Nature. 2014 Aug 7;512(7512):87-90. Pubmed
  • Oppenheim RD, Creek DJ, Macrae JI, Modrzynska KK, Pino P, Limenitakis J, Polonais V, Seeber F, Barrett MP, Billker O, McConville MJ, Soldati-Favre D. BCKDH: the missing link in apicomplexan mitochondrial metabolism is required for full virulence of Toxoplasma gondii and Plasmodium berghei. PLoS Pathog. 2014 Jul 17;10(7):e1004263. Pubmed
  • Pouchelon G, Gambino F, Bellone C, Telley L, Vitali I, Lüscher C, Holtmaat A, Jabaudon D. Modality-specific thalamocortical inputs instruct the identity of postsynaptic L4 neurons. Nature. 2014 Jul 24;511(7510):471-4. Pubmed
  • Quilodrán CS, Currat M, Montoya-Burgos JI. A general model of distant hybridization reveals the conditions for extinction in Atlantic salmon and brown trout. PLoS One. 2014 Jul 8;9(7):e101736. Pubmed
  • Sanchez-Mazas A, Meyer D. The relevance of HLA sequencing in population genetics studies. J Immunol Res. 2014;2014:971818. Pubmed
  • Santoni FA, Makrythanasis P, Nikolaev S, Guipponi M, Robyr D, Bottani A, Antonarakis SE. Simultaneous identification and prioritization of variants in familial, de novo, and somatic genetic disorders with VariantMaster. Genome Res. 2014 Feb;24(2):349-55. Pubmed
  • Villanyi Z, Ribaud V, Kassem S, Panasenko OO, Pahi Z, Gupta I, Steinmetz L, Boros I, Collart MA. The Not5 subunit of the ccr4-not complex connects transcription and translation. PLoS Genet. 2014 Oct 23;10(10):e1004569. Pubmed
  • Wenger Y, Buzgariu W, Reiter S, Galliot B. Injury-induced immune responses in Hydra. Semin Immunol. 2014 Jul 30. pii: S1044-5323(14)00061-X. Pubmed

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
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  • 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
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  • 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
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  • 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
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  • 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
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  • 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
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  • 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
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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