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

2022

  • Antonarakis SE. Short arms of human acrocentric chromosomes and the completion of the human genome sequence. Genome Res. 2022 Apr;32(4):599-607. Pubmed
  • Barbieri S, Nurni Ravi A, Griffin EE, Gotta M. Modeling protein dynamics in Caenorhabditis elegans embryos reveals that the PLK-1 gradient relies on weakly coupled reaction-diffusion mechanisms. Proc Natl Acad Sci U S A. 2022 Mar 15;119(11):e2114205119. Pubmed
  • Conod A, Silvano M, Ruiz I Altaba A. On the origin of metastases: Induction of pro-metastatic states after impending cell death via ER stress, reprogramming, and a cytokine storm. Cell Rep. 2022 Mar 8;38(10):110490. Pubmed
  • Darbellay F, Rouco R, Andrey G. MAZ regulates chromatin domain insulation and genome architecture. Nat Genet. 2022 Feb;54(2):96-97. Pubmed
  • Iwasaki M, Penfield S, Lopez-Molina L. Parental and environmental control of seed dormancy in Arabidopsis thaliana. Annu Rev Plant Biol. 2022 Feb 9. Online ahead of print. Pubmed
  • Miozzo F, Valencia-Alarcón EP, Stickley L, Majcin Dorcikova M, Petrelli F, Tas D, Loncle N, Nikonenko I, Bou Dib P, Nagoshi E. Maintenance of mitochondrial integrity in midbrain dopaminergic neurons governed by a conserved developmental transcription factor. Nat Commun. 2022 Mar 17;13(1):1426. Pubmed
  • Mohammadi Ghahhari N, Sznurkowska MK, Hulo N, Bernasconi L, Aceto N, Picard D. Cooperative interaction between ERα and the EMT-inducer ZEB1 reprograms breast cancer cells for bone metastasis. Nat Commun. 2022 Apr 19;13(1):2104. Pubmed
  • Nurk S, Koren S, Rhie A, Rautiainen M, Bzikadze AV, Mikheenko A, Vollger MR, Altemose N, Uralsky L, Gershman A, Aganezov S, Hoyt SJ, Diekhans M, Logsdon GA, Alonge M, Antonarakis SE, Borchers M, Bouffard GG, Brooks SY, Caldas GV, Chen NC, Cheng H, Chin CS, Chow W, de Lima LG, Dishuck PC, Durbin R, Dvorkina T, Fiddes IT, Formenti G, Fulton RS, Fungtammasan A, Garrison E, Grady PGS, Graves-Lindsay TA, Hall IM, Hansen NF, Hartley GA, Haukness M, Howe K, Hunkapiller MW, Jain C, Jain M, Jarvis ED, Kerpedjiev P, Kirsche M, Kolmogorov M, Korlach J, Kremitzki M, Li H, Maduro VV, Marschall T, McCartney AM, McDaniel J, Miller DE, Mullikin JC, Myers EW, Olson ND, Paten B, Peluso P, Pevzner PA, Porubsky D, Potapova T, Rogaev EI, Rosenfeld JA, Salzberg SL, Schneider VA, Sedlazeck FJ, Shafin K, Shew CJ, Shumate A, Sims Y, Smit AFA, Soto DC, Sović I, Storer JM, Streets A, Sullivan BA, Thibaud-Nissen F, Torrance J, Wagner J, Walenz BP, Wenger A, Wood JMD, Xiao C, Yan SM, Young AC, Zarate S, Surti U, McCoy RC, Dennis MY, Alexandrov IA, Gerton JL, O'Neill RJ, Timp W, Zook JM, Schatz MC, Eichler EE, Miga KH, Phillippy AM. The complete sequence of a human genome. Science. 2022 Apr;376(6588):44-53. Pubmed
  • Perez-Frances M, Abate MV, Baronnier D, Scherer PE, Fujitani Y, Thorel F, Herrera PL. Adult pancreatic islet endocrine cells emerge as fetal hormone-expressing cells. Cell Rep. 2022 Feb 15;38(7):110377. Pubmed
  • Romanova-Michaelides M, Hadjivasiliou Z, Aguilar-Hidalgo D, Basagiannis D, Seum C, Dubois M, Jülicher F, Gonzalez-Gaitan M. Morphogen gradient scaling by recycling of intracellular Dpp. Nature. 2022 Feb;602(7896):287-293. Pubmed
  • Solis GP, Kazemzadeh A, Abrami L, Valnohova J, Alvarez C, van der Goot FG, Katanaev VL. Local and substrate-specific S-palmitoylation determines subcellular localization of Gαo. Nat Commun. 2022 Apr 19;13(1):2072. Pubmed
  • Tzanoulinou S, Musardo S, Contestabile A, Bariselli S, Casarotto G, Magrinelli E, Jiang YH, Jabaudon D, Bellone C. Inhibition of Trpv4 rescues circuit and social deficits unmasked by acute inflammatory response in a Shank3 mouse model of Autism. Mol Psychiatry. 2022 Jan 12. Online ahead of print. Pubmed
  • Vafeiadou V, Hany D, Picard D. Hyperactivation of MAPK induces tamoxifen resistance in SPRED2-deficient ERα-positive breast cancer. Cancers (Basel). 2022 Feb 14;14(4):954. Pubmed
  • van Gurp L, Fodoulian L, Oropeza D, Furuyama K, Bru-Tari E, Vu AN, Kaddis JS, Rodríguez I, Thorel F, Herrera PL. Generation of human islet cell type-specific identity genesets. Nat Commun. 2022 Apr 19;13(1):2020. Pubmed
  • Zakany S, Smirnov S, Milinkovitch MC. Lizard skin patterns and the Ising model. Phys Rev Lett. 2022 Jan 27;128(4):048102. Pubmed

2021

  • Abbatemarco S, Bondaz A, Schwager F, Wang J, Hammell CM, Gotta M. PQN-59 and GTBP-1 contribute to stress granule formation but are not essential for their assembly in C. elegans embryos. J Cell Sci. 2021 Nov 15;134(22):jcs258834. Pubmed
  • Allais-Bonnet A, Hintermann A, Deloche MC, Cornette R, Bardou P, Naval-Sanchez M, Pinton A, Haruda A, Grohs C, Zakany J, Bigi D, Medugorac I, Putelat O, Greyvenstein O, Hadfield T, Jemaa SB, Bunevski G, Menzi F, Hirter N, Paris JM, Hedges J, Palhiere I, Rupp R, Lenstra JA, Gidney L, Lesur J, Schafberg R, Stache M, Wandhammer MD, Arbogast RM, Guintard C, Blin A, Boukadiri A, Rivière J, Esquerré D, Donnadieu C, Danchin-Burge C, Reich CM, Riley DG, van Marle-Koster E, Cockett N, Hayes BJ, Drögemüller C, Kijas J, Pailhoux E, Tosser-Klopp G, Duboule D, Capitan A. Analysis of polycerate mutants reveals the evolutionary co-option of HOXD1 for horn patterning in bovidae. Mol Biol Evol. 2021 May 19;38(6):2260-2272. Pubmed
  • Allen GE, Panasenko OO, Villanyi Z, Zagatti M, Weiss B, Pagliazzo L, Huch S, Polte C, Zahoran S, Hughes CS, Pelechano V, Ignatova Z, Collart MA. Not4 and Not5 modulate translation elongation by Rps7A ubiquitination, Rli1 moonlighting, and condensates that exclude eIF5A. Cell Rep. 2021 Aug 31;36(9):109633. Pubmed
  • Antonarakis SE, Holoubek A, Rapti M, Rademaker J, Meylan J, Iwaszkiewicz J, Zoete V, Wilson C, Taylor J, Ansar M, Borel C, Menzel O, Kuželová K, Santoni FA. Dominant monoallelic variant in the PAK2 gene causes Knobloch syndrome type 2. Hum Mol Genet. 2021 Dec 17;31(1):1-9. Pubmed
  • Bertiaux E, Balestra AC, Bournonville L, Louvel V, Maco B, Soldati-Favre D, Brochet M, Guichard P, Hamel V. Expansion microscopy provides new insights into the cytoskeleton of malaria parasites including the conservation of a conoid. PLoS Biol. 2021 Mar 11;19(3):e3001020. Pubmed
  • Cardoso YP, Jardim de Queiroz L, Bahechar IA, Posadas PE, Montoya-Burgos JI. Multilocus phylogeny and historical biogeography of Hypostomus shed light on the processes of fish diversification in La Plata Basin. Sci Rep. 2021 Mar 3;11(1):5073. Pubmed
  • Dagenais P, Hensman S, Haechler V, Milinkovitch MC. Elephants evolved strategies reducing the biomechanical complexity of their trunk. Curr Biol. 2021 Nov 8;31(21):4727-4737.e4. Pubmed
  • De Giorgi J, Fuchs C, Iwasaki M, Kim W, Piskurewicz U, Gully K, Utz-Pugin A, Mène-Saffrané L, Waridel P, Nawrath C, Longoni FP, Fujita S, Loubéry S, Lopez-Molina L. The Arabidopsis mature endosperm promotes seedling cuticle formation via release of sulfated peptides. Dev Cell. 2021 Nov 22;56(22):3066-3081.e5. Pubmed
  • Di D, Nunes JM, Jiang W, Sanchez-Mazas A. Like wings of a bird: functional divergence and complementarity between HLA-A and HLA-B molecules. Mol Biol Evol. 2021 Apr 13;38(4):1580-1594. Pubmed
  • Garcia A, Dunoyer-Geindre S, Fish RJ, Neerman-Arbez M, Reny JL, Fontana P. Methods to investigate miRNA function: focus on platelet reactivity. Thromb Haemost. 2021 Apr;121(4):409-421. Pubmed
  • Guerreiro A, De Sousa F, Liaudet N, Ivanova D, Eskat A, Meraldi P. WDR62 localizes katanin at spindle poles to ensure synchronous chromosome segregation. J Cell Biol. 2021 Aug 2;220(8):e202007171. Pubmed
  • Hannich JT, Loizides-Mangold U, Sinturel F, Harayama T, Vandereycken B, Saini C, Gosselin P, Brulhart-Meynet MC, Robert M, Chanon S, Durand C, Paz Montoya J, David FPA, Guessous I, Pataky Z, Golay A, Jornayvaz FR, Philippe J, Dermitzakis ET, Brown SA, Lefai E, Riezman H, Dibner C. Ether lipids, sphingolipids and toxic 1-deoxyceramides as hallmarks for lean and obese type 2 diabetic patients. Acta Physiol (Oxf). 2021 May;232(1):e13610. Pubmed
  • Istvan M, Rahban R, Dananche B, Senn A, Stettler E, Multigner L, Nef S, Garlantézec R. Maternal occupational exposure to endocrine-disrupting chemicals during pregnancy and semen parameters in adulthood: results of a nationwide cross-sectional study among Swiss conscripts. Hum Reprod. 2021 Jun 18;36(7):1948-1958. Pubmed
  • Iwasaki M, Lopez-Molina L. Arabidopsis thaliana mature endosperm dissection and isolation of genomic DNA from mature seed tissues. Methods Mol Biol. 2021;2250:239-243. Pubmed
  • Jaumouillé E, Koch R, Nagoshi E. Uncovering the roles of clocks and neural transmission in the resilience of Drosophila circadian network. Front Physiol. 2021 May 26;12:663339. Pubmed
  • Klingler E, Tomasello U, Prados J, Kebschull JM, Contestabile A, Galiñanes GL, Fièvre S, Santinha A, Platt R, Huber D, Dayer A, Bellone C, Jabaudon D. Temporal controls over inter-areal cortical projection neuron fate diversity. Nature. 2021 Nov;599(7885):453-457. Pubmed
  • Kulichová I, Mouterde M, Mokhtar MG, Diallo I, Tříska P, Diallo YM, Hofmanová Z, Poloni ES, Černý V. Demographic history was a formative mechanism of the genetic structure for the taste receptor TAS2R16 in human populations inhabiting Africa’s Sahel/Savannah Belt. Am J Phys Anthropol. 2021 Nov 30. Online ahead of print. Pubmed
  • Lemopoulos A, Montoya-Burgos JI. From scales to armor: Scale losses and trunk bony plate gains in ray-finned fishes. Evol Lett. 2021 Mar 23;5(3):240-250. Pubmed
  • Lentini G, Ben Chaabene R, Vadas O, Ramakrishnan C, Mukherjee B, Mehta V, Lunghi M, Grossmann J, Maco B, Visentin R, Hehl AB, Korkhov VM, Soldati-Favre D. Structural insights into an atypical secretory pathway kinase crucial for Toxoplasma gondii invasion. Nat Commun. 2021 Jun 18;12(1):3788. Pubmed
  • Li Y, Simmler LD, Van Zessen R, Flakowski J, Wan JX, Deng F, Li YL, Nautiyal KM, Pascoli V, Lüscher C. Synaptic mechanism underlying serotonin modulation of transition to cocaine addiction. Science. 2021 Sep 10;373(6560):1252-1256. Pubmed
  • Loizides-Mangold U, Petrenko V, Dibner C. Circadian lipidomics: analysis of lipid metabolites around the clock. Methods Mol Biol. 2021;2130:169-183. Pubmed
  • Machado Almeida P, Lago Solis B, Stickley L, Feidler A, Nagoshi E. Neurofibromin 1 in mushroom body neurons mediates circadian wake drive through activating cAMP-PKA signaling. Nat Commun. 2021 Oct 1;12(1):5758. Pubmed
  • Mancini V, Maeder J, Bortolin K, Schneider M, Schaer M, Eliez S. Long-term effects of early treatment with SSRIs on cognition and brain development in individuals with 22q11.2 deletion syndrome. Transl Psychiatry. 2021 May 29;11(1):336. Pubmed
  • Mayère C, Neirijnck Y, Sararols P, Rands CM, Stévant I, Kühne F, Chassot AA, Chaboissier MC, Dermitzakis ET, Nef S. Single-cell transcriptomics reveal temporal dynamics of critical regulators of germ cell fate during mouse sex determination. FASEB J. 2021 Apr;35(4):e21452. Pubmed
  • Mendel M, Delaney K, Pandey RR, Chen KM, Wenda JM, Vågbø CB, Steiner FA, Homolka D, Pillai RS. Splice site m6A methylation prevents binding of U2AF35 to inhibit RNA splicing. Cell. 2021 Jun 10;184(12):3125-3142.e25. Pubmed
  • Nunes JM. A comment on estimating HLA haplotype frequencies from homozygous individuals. Int J Immunogenet. 2021 Dec;48(6):496-497. Pubmed
  • Oropeza D, Cigliola V, Romero A, Chera S, Rodríguez-Seguí SA, Herrera PL. Stage-specific transcriptomic changes in pancreatic α-cells after massive β-cell loss. BMC Genomics. 2021 Aug 2;22(1):585. Pubmed
  • Perez-Frances M, van Gurp L, Abate MV, Cigliola V, Furuyama K, Bru-Tari E, Oropeza D, Carreaux T, Fujitani Y, Thorel F, Herrera PL. Pancreatic Ppy-expressing γ-cells display mixed phenotypic traits and the adaptive plasticity to engage insulin production. Nat Commun. 2021 Jul 22;12(1):4458. Pubmed
  • Podolec R, Demarsy E, Ulm R. Perception and signaling of ultraviolet-B radiation in plants. Annu Rev Plant Biol. 2021 Jun 17;72:793-822. Pubmed
  • Podolec R, Lau K, Wagnon TB, Hothorn M, Ulm R. A constitutively monomeric UVR8 photoreceptor confers enhanced UV-B photomorphogenesis. Proc Natl Acad Sci U S A. 2021 Feb 9;118(6):e2017284118. Pubmed
  • Prosée RF, Wenda JM, Özdemir I, Gabus C, Delaney K, Schwager F, Gotta M, Steiner FA. Transgenerational inheritance of centromere identity requires the CENP-A N-terminal tail in the C. elegans maternal germ line. PLoS Biol. 2021 Jul 6;19(7):e3000968. Pubmed
  • Quilodrán CS, Currat M, Montoya-Burgos JI. Air temperature influences early Covid-19 outbreak as indicated by worldwide mortality. Sci Total Environ. 2021 Oct 20;792:148312. Pubmed
  • Rio J, Quilodrán CS, Currat M. Spatially explicit paleogenomic simulations support cohabitation with limited admixture between Bronze Age Central European populations. Commun Biol. 2021 Oct 7;4(1):1163. Pubmed
  • Rouco R, Bompadre O, Rauseo A, Fazio O, Peraldi R, Thorel F, Andrey G. Cell-specific alterations in Pitx1 regulatory landscape activation caused by the loss of a single enhancer. Nat Commun. 2021 Dec 13;12(1):7235. Pubmed
  • Sandini C, Zöller D, Schneider M, Tarun A, Armondo M, Nelson B, Amminger PG, Yuen HP, Markulev C, Schäffer MR, Mossaheb N, Schlögelhofer M, Smesny S, Hickie IB, Berger GE, Chen EY, de Haan L, Nieman DH, Nordentoft M, Riecher-Rössler A, Verma S, Thompson A, Yung AR, McGorry PD, Van De Ville D, Eliez S. Characterization and prediction of clinical pathways of vulnerability to psychosis through graph signal processing. Elife. 2021 Sep 27;10:e59811. Pubmed
  • Sararols P, Stévant I, Neirijnck Y, Rebourcet D, Darbey A, Curley MK, Kühne F, Dermitzakis E, Smith LB, Nef S. Specific transcriptomic signatures and dual regulation of steroidogenesis between fetal and adult mouse Leydig cells. Front Cell Dev Biol. 2021 Jun 28;9:695546. Pubmed
  • Shore D, Zencir S, Albert B. Transcriptional control of ribosome biogenesis in yeast: links to growth and stress signals. Biochem Soc Trans. 2021 Aug 27;49(4):1589-1599. Pubmed
  • Shukla V, Han JP, Cléard F, Lefebvre-Legendre L, Gully K, Flis P, Berhin A, Andersen TG, Salt DE, Nawrath C, Barberon M. Suberin plasticity to developmental and exogenous cues is regulated by a set of MYB transcription factors. Proc Natl Acad Sci U S A. 2021 Sep 28;118(39):e2101730118. Pubmed
  • Shyian M, Shore D. Approaching protein barriers: Emerging mechanisms of replication pausing in eukaryotes. Front Cell Dev Biol. 2021 May 28;9:672510. Pubmed
  • Sinturel F, Gos P, Petrenko V, Hagedorn C, Kreppel F, Storch KF, Knutti D, Liani A, Weitz C, Emmenegger Y, Franken P, Bonacina L, Dibner C, Schibler U. Circadian hepatocyte clocks keep synchrony in the absence of a master pacemaker in the suprachiasmatic nucleus or other extrahepatic clocks. Genes Dev. 2021 Mar 1;35(5-6):329-334. Pubmed
  • Sklias A, Halaburkova A, Vanzan L, Jimenez NF, Cuenin C, Bouaoun L, Cahais V, Ythier V, Sallé A, Renard C, Durand G, Le Calvez-Kelm F, Khoueiry R, Murr R, Herceg Z. Epigenetic remodelling of enhancers in response to estrogen deprivation and re-stimulation. Nucleic Acids Res. 2021 Sep 27;49(17):9738-9754. Pubmed
  • Somm E, Montandon SA, Loizides-Mangold U, Gaïa N, Lazarevic V, De Vito C, Perroud E, Bochaton-Piallat ML, Dibner C, Schrenzel J, Jornayvaz FR. The GLP-1R agonist liraglutide limits hepatic lipotoxicity and inflammatory response in mice fed a methionine-choline deficient diet. Transl Res. 2021 Jan;227:75-88. Pubmed
  • Spiljar M, Steinbach K, Rigo D, Suárez-Zamorano N, Wagner I, Hadadi N, Vincenti I, Page N, Klimek B, Rochat MA, Kreutzfeldt M, Chevalier C, Stojanović O, Bejuy O, Colin D, Mack M, Cansever D, Greter M, Merkler D, Trajkovski M. Cold exposure protects from neuroinflammation through immunologic reprogramming. Cell Metab. 2021 Nov 2;33(11):2231-2246.e8. Pubmed
  • Stingi A, Cirillo L. SARS-CoV-2 infection and cancer: Evidence for and against a role of SARS-CoV-2 in cancer onset. Bioessays. 2021 Aug;43(8):e2000289. Pubmed
  • Stojanović O, Altirriba J, Rigo D, Spiljar M, Evrard E, Roska B, Fabbiano S, Zamboni N, Maechler P, Rohner-Jeanrenaud F, Trajkovski M. Dietary excess regulates absorption and surface of gut epithelium through intestinal PPARα. Nat Commun. 2021 Dec 2;12(1):7031. Pubmed
  • Suknovic N, Tomczyk S, Colevret D, Perruchoud C, Galliot B. The ULK1 kinase, a necessary component of the pro-regenerative and anti-aging machinery in Hydra. Mech Ageing Dev. 2021 Mar;194:111414. Pubmed
  • Vanzan L, Soldati H, Ythier V, Anand S, Braun SMG, Francis N, Murr R. High throughput screening identifies SOX2 as a super pioneer factor that inhibits DNA methylation maintenance at its binding sites. Nat Commun. 2021 Jun 7;12(1):3337. Pubmed
  • van Zessen R, Li Y, Marion-Poll L, Hulo N, Flakowski J, Lüscher C. Dynamic dichotomy of accumbal population activity underlies cocaine sensitization. Elife. 2021 Oct 5;10:e66048. Pubmed
  • Vilar R, Lukowski SW, Garieri M, Di Sanza C, Neerman-Arbez M, Fish RJ. Chemical modulators of fibrinogen production and their impact on venous thrombosis. Thromb Haemost. 2021 Apr;121(4):433-448. Pubmed
  • Vogg MC, Buzgariu W, Suknovic NS, Galliot B. Cellular, metabolic, and developmental dimensions of whole-body regeneration in Hydra. Cold Spring Harb Perspect Biol. 2021 Dec 1;13(12):a040725. Pubmed
  • Weiss B, Allen GE, Kloehn J, Abid K, Jaquier-Gubler P, Curran JA. eIF4E3 forms an active eIF4F complex during stresses (eIF4FS) targeting mTOR and re-programs the translatome. Nucleic Acids Res. 2021 May 21;49(9):5159-5176. Pubmed