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Research articles

Publications 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
  • 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
  • Galliot B, Crescenzi M, Jacinto A, Tajbakhsh S. Trends in tissue repair and regeneration. Development. 2017 Feb 1;144(3):357-364.  >>> 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
  • 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. TFIID or not TFIID, a continuing transcriptional SAGA. EMBO J. 2017 Feb 1;36(3):248-249.  >>> Journal
  • 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
  • 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
  • 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
  • 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
  • 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 May 24. [Epub ahead of print].  >>> 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
  • 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
  • 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


  • 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. Curr Top Microbiol Immunol. 2016 Sep 21. [Epub ahead of print].  >>> 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
  • Schalch T, Steiner FA. Structure of centromere chromatin: from nucleosome to chromosomal architecture. Chromosoma. 2016 Nov 17. [Epub ahead of print].  >>> 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
Latest modification: July 14, 2017 - 10 h 40

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