Publications

Publications 2019

Papers including work performed in the frame of iGE3

Alphabetical order of first authors’ names

  • Albert B, Kos-Braun IC, Henras AK, Dez C, Rueda MP, Zhang X, Gadal O, Kos M, Shore D. A ribosome assembly stress response regulates transcription to maintain proteome homeostasis. Elife. 2019 May 24;8. pii: e45002. ► Pubmed
  • Albert B, Tomassetti S, Gloor Y, Dilg D, Mattarocci S, Kubik S, Hafner L, Shore D. Sfp1 regulates transcriptional networks driving cell growth and division through multiple promoter-binding modes. Genes Dev. 2019 Mar 1;33(5-6):288-293. ► Pubmed
  • Ansar M, Chung HL, Al-Otaibi A, Elagabani MN, Ravenscroft TA, Paracha SA, Scholz R, Abdel Magid T, Sarwar MT, Shah SF, Qaisar AA, Makrythanasis P, Marcogliese PC, Kamsteeg EJ, Falconnet E, Ranza E, Santoni FA, Aldhalaan H, Al-Asmari A, Faqeih EA, Ahmed J, Kornau HC, Bellen HJ, Antonarakis SE. Bi-allelic variants in IQSEC1 cause intellectual disability, developmental delay, and short stature. Am J Hum Genet. 2019 Nov 7;105(5):907-920. ► Pubmed
  • Ansar M, Paracha SA, Serretti A, Sarwar MT, Khan J, Ranza E, Falconnet E, Iwaszkiewicz J, Shah SF, Qaisar AA, Santoni FA, Zoete V, Megarbane A, Ahmed J, Colombo R, Makrythanasis P, Antonarakis SE. Biallelic variants in FBXL3 cause intellectual disability, delayed motor development and short stature. Hum Mol Genet. 2019 Mar 15;28(6):972-979. ► Pubmed
  • Ansar M, Ullah F, Paracha SA, Adams DJ, Lai A, Pais L, Iwaszkiewicz J, Millan F, Sarwar MT, Agha Z, Shah SF, Qaisar AA, Falconnet E, Zoete V, Ranza E, Makrythanasis P, Santoni FA, Ahmed J, Katsanis N, Walsh C, Davis EE, Antonarakis SE. Bi-allelic variants in DYNC1I2 cause syndromic microcephaly with intellectual disability, cerebral malformations, and dysmorphic facial features. Am J Hum Genet. 2019 Jun 6;104(6):1073-1087. ► Pubmed
  • Bompadre O, Andrey G. Chromatin topology in development and disease. Curr Opin Genet Dev. 2019 Apr;55:32-38. ► Pubmed
  • Buhler S, Baldomero H, Ferrari-Lacraz S, Nunes JM, Sanchez-Mazas A, Massouridi-Levrat S, Heim D, Halter J, Nair G, Chalandon Y, Schanz U, Güngör T, Nicoloso G, Tiercy JM, Passweg J, Villard J. High-resolution HLA phased haplotype frequencies to predict the success of unrelated donor searches and clinical outcome following hematopoietic stem cell transplantation. Bone Marrow Transplant. 2019 Oct;54(10):1701-1709. ► Pubmed
  • Cordier T, Lanzén A, Apothéloz-Perret-Gentil L, Stoeck T, Pawlowski J. Embracing environmental genomics and machine learning for routine biomonitoring. Trends Microbiol. 2019 May;27(5):387-397. ► Pubmed
  • Currat M, Arenas M, Quilodran CS, Excoffier L, Ray N. SPLATCHE3: simulation of serial genetic data under spatially explicit evolutionary scenarios including long-distance dispersal. Bioinformatics. 2019 Nov 1;35(21):4480-4483. ► Pubmed
  • Damond N, Engler S, Zanotelli VRT, Schapiro D, Wasserfall CH, Kusmartseva I, Nick HS, Thorel F, Herrera PL, Atkinson MA, Bodenmiller B. A map of human type 1 diabetes progression by imaging mass cytometry. Cell Metab. 2019 Mar 5;29(3):755-768.e5. ► Pubmed
  • de Barsy M, Herrgott L, Martin V, Pillonel T, Viollier PH, Greub G. Identification of new DNA-associated proteins from Waddlia chondrophila. Sci Rep. 2019 Mar 20;9(1):4885. ► Pubmed
  • Delaneau O, Zagury JF, Robinson MR, Marchini JL, Dermitzakis ET. Accurate, scalable and integrative haplotype estimation. Nat Commun. 2019 Nov 28;10(1):5436. ► Pubmed
  • Delaneau O, Zazhytska M, Borel C, Giannuzzi G, Rey G, Howald C, Kumar S, Ongen H, Popadin K, Marbach D, Ambrosini G, Bielser D, Hacker D, Romano L, Ribaux P, Wiederkehr M, Falconnet E, Bucher P, Bergmann S, Antonarakis SE, Reymond A, Dermitzakis ET. Chromatin three-dimensional interactions mediate genetic effects on gene expression. Science. 2019 May 3;364(6439). ► Pubmed
  • Delaney K, Strobino M, Wenda JM, Pankowski A, Steiner FA. H3.3K27M-induced chromatin changes drive ectopic replication through misregulation of the JNK pathway in C. elegans. Nat Commun. 2019 Jun 7;10(1):2529. ► Pubmed
  • Furuyama K, Chera S, van Gurp L, Oropeza D, Ghila L, Damond N, Vethe H, Paulo JA, Joosten AM, Berney T, Bosco D, Dorrell C, Grompe M, Ræder H, Roep BO, Thorel F, Herrera PL. Diabetes relief in mice by glucose-sensing insulin-secreting human α-cells. Nature. 2019 Mar;567(7746):43-48. ► Pubmed
  • Gambarotto D, Zwettler FU, Le Guennec M, Schmidt-Cernohorska M, Fortun D, Borgers S, Heine J, Schloetel JG, Reuss M, Unser M, Boyden ES, Sauer M, Hamel V, Guichard P. Imaging cellular ultrastructures using expansion microscopy (U-ExM). Nat Methods. 2019 Jan;16(1):71-74. ► Pubmed
  • Hafner L, Shore D, Mattarocci S. ChECing out Rif1 action in freely cycling cells. Curr Genet. 2019 Apr;65(2):429-434. ► Pubmed
  • Hannich JT, Galih Haribowo A, Gentina S, Paillard M, Gomez L, Pillot B, Thibault H, Abegg D, Guex N, Zumbuehl A, Adibekian A, Ovize M, Martinou J-C, Riezman H. 1-deoxydihydroceramide causes anoxic death by impairing chaperonin-mediated protein folding. Nat Metab. 2019 Oct;1(10):996-1008. ► Pubmed
  • Haribowo AG, Hannich JT, Michel AH, Megyeri M, Schuldiner M, Kornmann B, Riezman H. Cytotoxicity of 1-deoxysphingolipid unraveled by genome-wide genetic screens and lipidomics in Saccharomyces cerevisiae. Mol Biol Cell. 2019 Oct 15;30(22):2814-2826. ► Pubmed
  • Ho WKW, Freem L, Zhao D, Painter KJ, Woolley TE, Gaffney EA, McGrew MJ, Tzika A, Milinkovitch MC, Schneider P, Drusko A, Matthäus F, Glover JD, Wells KL, Johansson JA, Davey MG, Sang HM, Clinton M, Headon DJ. Feather arrays are patterned by interacting signalling and cell density waves. PLoS Biol. 2019 Feb 21;17(2):e3000132. ► Pubmed
  • Infantino V, Tutucci E, Yeh Martin N, Zihlmann A, Garcia-Molinero V, Silvano G, Palancade B, Stutz F. The mRNA export adaptor Yra1 contributes to DNA double-strand break repair through its C-box domain. PLoS One. 2019 Apr 5;14(4):e0206336. ► Pubmed
  • Iwasaki M, Hyvärinen L, Piskurewicz U, Lopez-Molina L. Non-canonical RNA-directed DNA methylation participates in maternal and environmental control of seed dormancy. Elife. 2019 Mar 26;8. pii: e37434. ► Pubmed
  • Kim W, Zeljković SĆ, Piskurewicz U, Megies C, Tarkowski P, Lopez-Molina L. Polyamine uptake transporter 2 (put2) and decaying seeds enhance phyA-mediated germination by overcoming PIF1 repression of germination. PLoS Genet. 2019 Jul 24;15(7):e1008292. ► Pubmed
  • Kubik S, Bruzzone MJ, Challal D, Dreos R, Mattarocci S, Bucher P, Libri D, Shore D. Opposing chromatin remodelers control transcription initiation frequency and start site selection. Nat Struct Mol Biol. 2019 Aug;26(8):744-754. ► Pubmed
  • Lau K, Podolec R, Chappuis R, Ulm R, Hothorn M. Plant photoreceptors and their signaling components compete for COP1 binding via VP peptide motifs. EMBO J. 2019 Sep 16;38(18):e102140. ► Pubmed
  • Longoni P, Samol I, Goldschmidt-Clermont M. The kinase STATE TRANSITION 8 phosphorylates light harvesting complex II and contributes to light acclimation in Arabidopsis thaliana. Front Plant Sci. 2019 Sep 19;10:1156. ► Pubmed
  • Loureiro M, Achargui R, Flakowski J, Van Zessen R, Stefanelli T, Pascoli V, Lüscher C. Social transmission of food safety depends on synaptic plasticity in the prefrontal cortex. Science. 2019 Jun 7;364(6444):991-995. ► Pubmed
  • MacGregor DR, Zhang N, Iwasaki M, Chen M, Dave A, Lopez-Molina L, Penfield S. ICE1 and ZOU determine the depth of primary seed dormancy in Arabidopsis independently of their role in endosperm development. Plant J. 2019 Apr;98(2):277-290. ► Pubmed
  • Megyeri M, Prasad R, Volpert G, Sliwa-Gonzalez A, Haribowo AG, Aguilera-Romero A, Riezman H, Barral Y, Futerman AH, Schuldiner M. Yeast ceramide synthases, Lag1 and Lac1, have distinct substrate specificity. J Cell Sci. 2019 Jun 24;132(12):jcs228411. ► Pubmed
  • Montandon SA, Fofonjka A, Milinkovitch MC. Elastic instability during branchial ectoderm development causes folding of the Chlamydosaurus erectile frill. Elife. 2019 Jun 25;8. pii: e44455. ► Pubmed
  • Montandon SA, Somm E, Loizides-Mangold U, de Vito C, Dibner C, Jornayvaz FR. Multi-technique comparison of atherogenic and MCD NASH models highlights changes in sphingolipid metabolism. Sci Rep. 2019 Nov 14;9(1):16810. ► Pubmed
  • Oberst P, Fièvre S, Baumann N, Concetti C, Bartolini G, Jabaudon D. Temporal plasticity of apical progenitors in the developing mouse neocortex. Nature. 2019 Sep;573(7774):370-374. ► Pubmed
  • Panasenko OO, Somasekharan SP, Villanyi Z, Zagatti M, Bezrukov F, Rashpa R, Cornut J, Iqbal J, Longis M, Carl SH, Peña C, Panse VG, Collart MA. Co-translational assembly of proteasome subunits in NOT1-containing assemblysomes. Nat Struct Mol Biol. 2019 Feb;26(2):110-120. ► Pubmed
  • Panousis NI, Bertsias GK, Ongen H, Gergianaki I, Tektonidou MG, Trachana M, Romano-Palumbo L, Bielser D, Howald C, Pamfil C, Fanouriakis A, Kosmara D, Repa A, Sidiropoulos P, Dermitzakis ET, Boumpas DT. Combined genetic and transcriptome analysis of patients with SLE: distinct, targetable signatures for susceptibility and severity. Ann Rheum Dis. 2019 Aug;78(8):1079-1089. ► Pubmed
  • Prouteau M, Loewith R. TOR signaling is going through a phase. Cell Metab. 2019 May 7;29(5):1019-1021. ► Pubmed
  • Quilodrán CS, Nussberger B, Montoya-Burgos JI, Currat M. Hybridization and introgression during density-dependent range expansion: European wildcats as a case study. Evolution. 2019 Apr;73(4):750-761. ► Pubmed
  • Rahban R, Priskorn L, Senn A, Stettler E, Galli F, Vargas J, Van den Bergh M, Fusconi A, Garlantezec R, Jensen TK, Multigner L, Skakkebaek NE, Germond M, Jørgensen N, Nef S; NICER Working Group. Semen quality of young men in Switzerland: a nationwide cross-sectional population-based study. Andrology. 2019 Nov;7(6):818-826. ► Pubmed
  • Rentzsch F, Juliano C, Galliot B. Modern genomic tools reveal the structural and cellular diversity of cnidarian nervous systems. Curr Opin Neurobiol. 2019 Jun;56:87-96. ► Pubmed
  • Riggi M, Bourgoint C, Macchione M, Matile S, Loewith R, Roux A. TORC2 controls endocytosis through plasma membrane tension. J Cell Biol. 2019 Jul 1;218(7):2265-2276. ► Pubmed
  • Rivera-Rivera CJ, Montoya-Burgos JI. LSX: automated reduction of gene-specific lineage evolutionary rate heterogeneity for multi-gene phylogeny inference. BMC Bioinformatics. 2019 Aug 13;20(1):420. ► Pubmed
  • Sadowski SM, Petrenko V, Meyer P, Pusztaszeri M, Brulhart-Meynet MC, Heddad Masson M, Triponez F, Philippe J, Dibner C. Validation of molecular biomarkers for preoperative diagnostics of human papillary thyroid carcinoma in fine needle aspirates. Gland Surg. 2019 Aug;8(Suppl 2):S62-S76. ► Pubmed
  • Sanchez-Mazas A, Nunes JM. Does NGS typing highlight our understanding of HLA population diversity?: Some good reasons to say yes and a few to say be careful. Hum Immunol. 2019 Jan;80(1):62-66. ► Pubmed
  • Schibler M, Brito F, Zanella MC, Zdobnov EM, Laubscher F, L'Huillier AG, Ambrosioni J, Wagner N, Posfay-Barbe KM, Docquier M, Schiffer E, Savoldelli GL, Fournier R, Lenggenhager L, Cordey S, Kaiser L. Viral sequences detection by high-throughput sequencing in cerebrospinal fluid of individuals with and without central nervous system disease. Genes (Basel). 2019 Aug 19;10(8). pii: E625. ► Pubmed
  • Schmidt-Cernohorska M, Zhernov I, Steib E, Le Guennec M, Achek R, Borgers S, Demurtas D, Mouawad L, Lansky Z, Hamel V, Guichard P. Flagellar microtubule doublet assembly in vitro reveals a regulatory role of tubulin C-terminal tails. Science. 2019 Jan 18;363(6424):285-288. ► Pubmed
  • Sinturel F, Makhlouf AM, Meyer P, Tran C, Pataky Z, Golay A, Rey G, Howald C, Dermitzakis ET, Pichard C, Philippe J, Brown SA, Dibner C. Cellular circadian period length inversely correlates with HbA1c levels in individuals with type 2 diabetes. Diabetologia. 2019 Aug;62(8):1453-1462. ► Pubmed
  • Soudet J, Stutz F. Regulation of gene expression and replication initiation by non-coding transcription: a model based on reshaping nucleosome-depleted regions: influence of pervasive transcription on chromatin structure. Bioessays. 2019 Nov;41(11):e1900043. ► Pubmed
  • Stamoulis G, Garieri M, Makrythanasis P, Letourneau A, Guipponi M, Panousis N, Sloan-Béna F, Falconnet E, Ribaux P, Borel C, Santoni F, Antonarakis SE. Single cell transcriptome in aneuploidies reveals mechanisms of gene dosage imbalance. Nat Commun. 2019 Oct 3;10(1):4495. ► Pubmed
  • Stanway RR, Bushell E, Chiappino-Pepe A, Roques M, Sanderson T, Franke-Fayard B, Caldelari R, Golomingi M, Nyonda M, Pandey V, Schwach F, Chevalley S, Ramesar J, Metcalf T, Herd C, Burda PC, Rayner JC, Soldati-Favre D, Janse CJ, Hatzimanikatis V, Billker O, Heussler VT. Genome-scale identification of essential metabolic processes for targeting the Plasmodium liver stage. Cell. 2019 Nov 14;179(5):1112-1128.e26. ► Pubmed
  • Stévant I, Kühne F, Greenfield A, Chaboissier MC, Dermitzakis ET, Nef S. Dissecting cell lineage specification and sex fate determination in gonadal somatic cells using single-cell transcriptomics. Cell Rep. 2019 Mar 19;26(12):3272-3283.e3. ► Pubmed
  • Stévant I, Nef S. Genetic control of gonadal sex determination and development. Trends Genet. 2019 May;35(5):346-358. ► Pubmed
  • Stojanović O, Trajkovski M. Microbiota guides insulin trafficking in beta cells. Cell Res. 2019 Aug;29(8):603-604. ► Pubmed
  • Telley L, Agirman G, Prados J, Amberg N, Fièvre S, Oberst P, Bartolini G, Vitali I, Cadilhac C, Hippenmeyer S, Nguyen L, Dayer A, Jabaudon D. Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex. Science. 2019 May 10;364(6440). ► Pubmed
  • Tomczyk S, Buzgariu W, Perruchoud C, Fisher K, Austad S, Galliot B. Loss of neurogenesis in aging Hydra. Dev Neurobiol. 2019 May;79(5):479-496. ► Pubmed
  • Vangenot C, Gagneux P, de Groot NG, Baumeyer A, Mouterde M, Crouau-Roy B, Darlu P, Sanchez-Mazas A, Sabbagh A, Poloni ES. Humans and chimpanzees display opposite patterns of diversity in arylamine N-acetyltransferase genes. G3 (Bethesda). 2019 Jul 9;9(7):2199-2224. ► Pubmed
  • Vogg MC, Beccari L, Iglesias Ollé L, Rampon C, Vriz S, Perruchoud C, Wenger Y, Galliot B. An evolutionarily-conserved Wnt3/β-catenin/Sp5 feedback loop restricts head organizer activity in Hydra. Nat Commun. 2019 Jan 18;10(1):312. ► Pubmed
  • Vogg MC, Galliot B, Tsiairis CD. Model systems for regeneration: Hydra. Development. 2019 Nov 1;146(21). pii: dev177212. ► Pubmed
  • Weiss A, Le Roux-Bourdieu M, Zoetemelk M, Ramzy GM, Rausch M, Harry D, Miljkovic-Licina M, Falamaki K, Wehrle-Haller B, Meraldi P, Nowak-Sliwinska P. Identification of a synergistic multi-drug combination active in cancer cells via the prevention of spindle pole clustering. Cancers (Basel). 2019 Oct 22;11(10):1612. ► Pubmed
  • Wilhelm T, Olziersky AM, Harry D, De Sousa F, Vassal H, Eskat A, Meraldi P. Mild replication stress causes chromosome mis-segregation via premature centriole disengagement. Nat Commun. 2019 Aug 8;10(1):3585. ► Pubmed

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