Disclaimer: This page includes all preprints by NCCR member labs.
Preprints
- L.-A. Gurzeler, M. Link, Y. Ibig, I. Schmidt, O. Galuba, J. Schoenbett, C. Gasser-Didierlaurant, C.N. Parker, X. Mao,F. Bitsch, M. Schirle, P. Couttet, F. Sigoillot, J. Ziegelmüller, A.-C. Uldry, N. Schmiedeberg, O. Mühlemann and J. Reinhardt (2023) Drug-induced eRF1 degradation promotes readthrough and reveals a new branch of ribosome quality control
bioRxiv - F. Lodi, M. Certo, H. Elkafrawy, W. Li, H.A. Vu, K. Gilbo, L. Su, I.L. Pegg, T. Weiss, M. Bühler, M. Weller, C. Yeh, J.E. Corn, K.-S.E. Park, J.-H. Ko, J. Behmoaras, C. Mauro, D. Lambrechts and A.E. Papathanassiu (2023) BCAT1 inhibition affects CD8+ T cell activation, exhaustion, and tumoral immunity by altering iron homeostasis
bioRxiv - A. Brkic, M. Leibundgut, J. Jablonska, V. Zanki, Z. Car, V. Petrovic-Perokovic, A. Maršavelski, N. Ban and I. Gruic-Sovulj (2023) Antibiotic hyper-resistance in a class I aminoacyl-tRNA synthetase with altered active site signature motif
bioRxiv - M.Y. Boontanrart, E. Mächler, S. Ponta, J.C. Nelis, V.G. Preiano and J.E. Corn (2022) Engineering of the Endogenous HBD promoter increases HbA2
bioRxiv - C. Wenger, A. Harsman, M. Niemann, S. Oeljeklaus, C. von Känel, S. Calderaro, B. Warscheid and A. Schneider (2022) The Mba1 homologue of Trypanosoma brucei is involved in the biogenesis of oxidative phosphorylation complexes
bioRxiv - M.E. Karasu, E. Toufektchan, J. Maciejowski and J.E. Corn (2022) TREX1 restricts CRISPR-Cas9 genome editing in human cells
bioRxiv - A. Daniels, S.L. Fletcher, H. Kerr, A. Kratzel, N. Kriplani, N. Craig, J.C. Hastie, P. Digard, P. Davies, V. Thiel and C. Tait-Burkard (2022) One for all – Human kidney Caki-1 cells are highly susceptible to infection with corona- and other respiratory viruses
bioRxiv - M. Jaskolowski, A. Jomaa, M. Gamerdinger, S. Shrestha, M. Leibundgut, E. Deuerling and N. Ban (2022) Molecular basis of the TRAP complex function in ER protein biogenesis
bioRxiv - R. Abdelnabi, D. Jochmans, K. Donckers, B. Trueeb, N. Ebert, B. Weynand, V. Thiel and J. Neyts (2022) Nirmatrelvir-resistant SARS-CoV-2 is efficiently transmitted in Syrian hamsters
bioRxiv - A. Meindl, M. Romberger, G. Lehmann, N. Eichner, L. Kleemann, J. Wu, J. Danner, M. Boesl, M. Mesitov, G. Meister, J. Koenig, S. Leidel and J. Medenbach (2022) A rapid protocol for ribosome profiling of low input samples
bioRxiv - B. Mhlekude, D. Postmus, J. Weiner III, S. Stenzel, F.J. Zapatero-Belinchon, R. Olmer, J. Jansen, A. Richter, J. Heinze, N. Heinemann, B. Muhlemann, S. Schroeder, T.C. Jones, M.A. Muller, C. Drosten, A. Pich, V. Thiel, U. Martin, D. Niemeyer, G. Gerold, D. Beule and C. Goffinet (2022) Pharmacological inhibition of bromodomain and extra-terminal proteins induces NRF-2-mediated inhibition of SARS-CoV-2 replication and is subject to viral antagonism
bioRxiv - P. Chouvardas, M. Zimmerli, D. Hanhart, M. Moser, H.A. Guillen-Ramirez, S. Mishra, R. Esposito, T. Polidori, M. Widmer, R. Garcia-Perez, M. Kruithof-de Julio, D.D. Pervouchine, M. Mele and R. Johnson (2022) TransCistor reveals the landscape of cis-regulatory long noncoding RNAs
bioRxiv - G. Padroni, M. Bikaki, M. Novakovic, A.C. Wolter, S.H. Rüdisser, A.D. Gossert, A. Leitner and F.H.-T Allain (2022) A hybrid structure determination approach to investigate the druggability of the nucleocapsid protein of SARS-CoV-2
bioRxiv - A. Saha, M. Ahsan, P.R. Arantes, M. Schmitz, C. Chanez, M. Jinek and G. Palermo (2022) An Alpha-helical Lid Guides the Target DNA toward Catalysis in CRISPR-Cas12a
bioRxiv - A. Vancura, A.H. Gutierrez, T. Hennig, C. Pulido-Quetglas, F. Slack, R. Johnson and S. Haefliger (2022) Is evolutionary conservation a useful predictor for cancer long noncoding RNAs? Insights from the Cancer lncRNA Census 3
bioRxiv - S. Campagne, D. Jutzi, F. Malard, M. Matoga, K. Romane, M. Feldmuller, M. Colombo, M.-D. Ruepp and F.H.-T. Allain (2022) The cancer-associated RBM39 bridges the pre-mRNA, U1 and U2 snRNPs to regulate alternative splicing
bioRxiv - G. Dias de Melo, V. Perraud, F. Alvarez, A. Vieites-Prado, S. Kim, L. Kergoat, B.S. Trueb, M. Tichit, A. Piazza, A. Thierry, D. Hardy, N. Wolff, S. Munier, R. Koszul, E. Simon-Loriere, V. Thiel, M. Lecuit, P.-M. Lledo, N. Renier, F. Larrous and H. Bourhy (2022) Neuroinvasion and anosmia are independent phenomena upon infection with SARS-CoV-2 and its variants
bioRxiv - J. Farnung, M. Muhar, J. R. Liang, K.A. Tolmachova, R.M. Benoit, J.E. Corn and J.W. Bode (2022) Human ATG3 contains a non-canonical LIR motif crucial for its enzymatic activity in autophagy
bioRxiv - K. M. Thumfart, S. Lazzeri, F. Manuella and I. Mansuy (2022) Long-term effects of early postnatal stress on Sertoli cells functions
bioRxiv - G. Dorn, C. Gmeiner, T. de Vries, E. Dedic, M. Novakovic, F.F. Damberger, C. Maris, E. Finol, C.P. Sarnowski, J. Kolhbrecher, T.J. Welsh, S. Bolisetty, R. Mezzenga, R. Aebersold, A. Leitner, M. Yulikov, G. Jeschke and F.H.-T. Allain (2022) Integrative solution structure of a PTBP1-viral IRES complex reveals strong compaction and ordering with residual conformational flexibility
bioRxiv - M. Katsantoni, E.J. van Nimwegen and M. Zavolan (2022) Improved analysis of (e)CLIP data with RCRUNCH yields a compendium of RNA-binding protein binding sites and motifs
bioRxiv - G. Katsioudi, R. Dreos, E.S. Arpa, S. Gaspari, A. Liechti, M. Sato, C.H. Gabriel, A. Kramer, S.A. Brown and D. Gatfield (2022) A novel Smg6 mouse model reveals regulation of circadian period and daily CRY2 accumulation through the nonsense-mediated mRNA decay pathway
bioRxiv - M. Schmitz, I. Querques, S. Oberli, C. Chanez and M. Jinek (2022) Structural basis for RNA-mediated assembly of type V CRISPR-associated transposons
bioRxiv - P. Simmler, T. Mengis, K. Van-Lehmann, A. Khales, T. Thomas, G. Rätsch, M. Stoffel and G. Schwank (2022) Mutant SF3B1 promotes PDAC malignancy through TGF-B resistance
bioRxiv - A. Taddeo, I. Berenguer Veiga, C. Devisme, R. Boss, P. Plattet, S. Weigang, G. Kochs, V. Thiel, C. Benarafa and G. Zimmer (2022) Optimized intramuscular immunization with VSV-vectored spike protein triggers a superior protective humoral immune response to SARS-CoV-2
bioRxiv - D. Jochmans, C. Liu, K. Donckers, A. Stoycheva, S. Boland, S.K. Stevens, C. De Vita, B. Vanmechelen, P. Maes, B.S. Trüeb, N. Ebert, V. Thiel, S. De Jonghe, L. Vangeel, D. Bardiot, A. Jekle, L.M. Blatt, L. Beigelman, J.A. Symons, P. Raboisson, P. Chaltin, A. Marchand, J. Neyts, J. Deval and K. Vandyck (2022) The substitutions L50F, E166A and L167F in SARS-CoV-2 3CLpro are selected by a protease inhibitor in vitro and confer resistance to nirmatrelvir
bioRxiv - L.M. Muckenfuss, A.C. Migenda Herranz, F.M. Boneberg, M. Clerici and M. Jinek (2022) Fip1 is a multivalent interaction scaffold for processing factors in human mRNA 3' end biogenesis
bioRxiv - J. Breda, A. Banerjee, J. Pieters, R. Jayachandran and M. Zavolan (2022) A novel approach to single cell analysis to reveal intrinsic differences in immune marker expression in unstimulated macrophages from BALB/c and C57BL/6 mouse strains
bioRxiv - A. Moursy, A. Cléry, S. Gerhardy, K.M. Betz, S. Rao, S. Campagne, I. Beusch, M.M. Duszczyk, M.D. Robinson, V.G. Panse and F. H.-T. Allain (2022) The structure of yeast Npl3 bound to RNA reveals a cooperative sequence-specific recognition and an RNA chaperone role in splicing
bioRxiv - Manuela Pérez-Berlanga, V.I. Wiersma, A. Zbinden, L. De Vos, U. Wagner, C. Foglieni, I. Mallona, K.M. Betz, A. Cléry, J. Weber, Z. Guo, R. Rigort, P. de Rossi, R. Manglunia, E. Tantardini, S. Sahadevan, O. Stach, M. Hruska-Plochan, F.H.-T. Allain, P. Paganetti and M. Polymenidou (2022) TDP-43 oligomerization and RNA binding are codependent but their loss elicits distinct pathologies
bioRxiv - A.D. Holmes, P.P. Chan, Q. Chen, P. Ivanov, L. Drouard, N. Polacek, M.A. Kay and T.M. Lowe (2022) A Standardized Ontology for Naming tRNA-derived RNAs Based on Molecular Origin
bioRxiv - T. Barut, N.J. Halwe, A. Taddeo, J.N. Kelly, J. Schön, N. Ebert, L. Ulrich, C. Devisme, S. Steiner, B.S. Trueeb, B. Hoffmann, I. Berenguer Veiga, N. François G. Leborgne, E. Aquiar Moreira, A. Breithaupt, C. Wylezich, D. Höper, K. Wernike, A. Godel, L. Thomann, V. Flück, H. Stalder, M. Brügger, B.I. Oliveira Esteves, B. Zumkehr, G. Beilleau, A. Kratzel, K. Schmied, S. Ochsenbein, R.M. Lang, M. Wider, C. Machahua, P. Dorn, T.M. Marti, M. Funke-Chambour, A. Rauch, M. Widera, S. Ciesek, R. Dijkman, D. Hoffmann, M.P. Alves, C. Benarafa, M. Beer and V. Thiel (2022) The spike gene is a major determinant for the SARS-CoV-2 Omicron-BA.1 phenotype
bioRxiv - J. Beer, S. Crotta, A. Breithaupt, A. Ohnemus, J. Becker, B. Sachs, L. Kern, M. Llorian, N. Ebert, F. Labroussaa, T.T.N. Tran, B.S. Trueeb, J. Jores, V. Thiel, M. Beer, J. Fuchs, G. Kochs, A. Wack, M. Schwemmle and D. Schnepf (2022) Impaired immune response drives age-dependent severity of COVID-19
bioRxiv - S.M. Siegner, A. Clemens, L. Ugalde, L. Garcia-Garcia, J.A. Bueren, P. Rio, M.E. Karasu, and J.E. Corn (2022) Adenine base editing is an efficient approach to restore function in FA patient cells without double-stranded DNA breaks
bioRxiv - C.P. Sarnowski, A. Knörlein, Tebbe de Vries, M, Götze, I. Beusch, R. Aebersold, F.H.-T. Allain, J. Hall and A. Leitner (2022) Sensitive detection and structural characterisation of UV-induced cross-links in protein-RNA complexes using CLIR-MS
bioRxiv - P. Brandys, X. Montagutelli, I. Merenkova, G.T. Barut, V. Thiel, N.J. Schork, B. Trüeb, L. Conquet, A. Deng, A. Antanasijevic, H.-K. Lee, M. Valière, A. Sindhu, G. Singh and J. Herold (2022) A mRNA vaccine encoding for a RBD 60-mer nanoparticle elicits neutralizing antibodies and protective immunity against the SARS-CoV-2 delta variant in transgenic K18-hACE2 mice
bioRxiv - I. Ritsch, E. Lehmann, L. Emmanouilidis, M. Yulikov, F. Allain and G. Jeschke (2022) Phase separation of hnRNP A1 upon specific RNA-binding observed by magnetic resonance
bioRxiv - S. Martinez, R. Weber, T. Woo, A. Malik, M. Geuenich, G. H. Jang, D. Dervovic, K. Al-Zahrani, R. Tsai, N. Fodil, P. Gros, S.S. Sidhu, S. Gallinger, G. Neely, K. Campbell, F. Notta, A. Sendoel and D. Schramek (2022) In vivo CRISPR screens reveal SCAF1 and USP15 as novel drivers of pancreatic cancer
bioRxiv - S. Aeschlimann, A. Kalichava, B. Schimanski, P. Stettler, T. Ochsenreiter and A. Schneider (2022) The mitochondrial genome segregation system of T. brucei: Single p197 molecules connect the basal body with the outer membrane
bioRxiv - M.W.M. Meeuse, S. Nahar, K.n Braun and H. Grosshans (2022) The Grainyhead/LSF transcription factor GRH-1 is rhythmically required for molting
bioRxiv - M. Avar, D. Heinzer, A.M. Thackray, Y. Liu, M. Hruska-Plochan, S. Sellitto, E. Schaper, D.P. Pease, J.-A. Yin, A.K.K. Lakkaraju, M. Emmenegger, M. Losa, A. Chincisan, S. Hornemann, M. Polymenidou, R. Bujdoso and A. Aguzzi (2022) An Arrayed Genome-Wide Perturbation Screen Identifies the Ribonucleoprotein hnRNP K As Rate-Limiting for Prion Propagation
bioRxiv - N. Raad, D. Tandon, S. Hapfelmeier and N. Polacek (2022) The stationary phase-specific sRNA fimR2 is a multifunctional regulator of bacterial motility, biofilm formation and virulence
bioRxiv - B. Hurwitz, N. Guzzi, A. Gola, V.F. Fiore, A. Sendoel, M. Nikolova, D. Barrows, T.S. Carroll, H. Amalia Pasolli and E. Fuchs (2022) The integrated stress response remodels the microtubule organizing center to clear unfolded proteins following proteotoxic stress
bioRxiv - V. Zanki, B. Bozic, M. Mocibob, N. Ban and I. Gruic-Sovulj (2022) A pair of isoleucyl-tRNA synthetases in Bacilli fulfill complementary roles to enhance fitness and provide antibiotic resistance
bioRxiv - M. Flemr, M. Schwaiger, D. Hess, V. Iesmantavicius, A.C. Tuck, F. Mohn and M. Buehler (2022) Mouse Nuclear RNAi-defective 2 Promotes Splicing of Weak 5' Splice Sites
bioRxiv - M. Jambeau, K.D. Meyer, M. Hruska-Plochan, R. Tabet, C.-Z. Lee, A. Ray-Soni, C. Aguilar, K. Savage, N. Mishra, N. Cavegn, P. Borter, C.-C. Lin, K. Jansen-West, J. Jiang, F. Freyermuth, N. Li, P. De Rossi, M. Pérez-Berlanga, X. Jiang, L.M. Daughrity, J. Pereira, S. Narayanan, Y. Gu, S. Dhokai, I. Dalkilic-Liddle, Z. Maniecka, J. Weber, M. Workman, M. McAlonis-Downes, E. Berezovski, Y.-J. Zhang, J. Berry, B.J. Wainger, M.W. Kankel, M. Rushe, C. Hock, R.M. Nitsch, D.W. Cleveland, L. Petrucelli, T. Gendron, F. Montrasio, J. Grimm, M. Polymenidou and Clotilde Lagier-Tourenne (2022) Comprehensive preclinical evaluation of human-derived anti-poly-GA antibodies in cellular and animal models of C9ORF72 disease
bioRxiv - M. Bak, E. van Nimwegen, R. Schmidt, M. Zavolan and A.J. Gruber (2022) Frequent co-regulation of splicing and polyadenylation by RNA-binding proteins inferred with MAPP
bioRxiv - A. Singh, X.X. Maurer-Alcalá, T. Solberg, S. Gisler, M. Ignarski, E.C. Swart and M. Nowacki (2022) RNA-mediated nucleosome depletion is required for elimination of transposon-derived DNA
bioRxiv - B. Schimanski, S. Aeschlimann, S. Käser, M. Gomez-Fabra Gala, N. Vögtle and A. Schneider (2021) p166 links membrane and intramitochondrial modules of the trypanosomal tripartite attachment complex
bioRxiv - M. Hruska-Plochan, K.M. Hembach, S. Ronchi, V.I. Wiersma, Z. Maniecka, E.-M. Hock, F. Laferriere, S. Sahadevan, V. Hoop, I. Delvendahl, M. Panatta, A. van der Bourg, D. Bohaciakova, K. Frontzek, A. Aguzzi, T. Lashley, M.D. Robinson, T. Karayannis, M. Mueller, A. Hierlemann and M. Polymenidou (2021) Human neural networks with sparse TDP-43 pathology reveal NPTX2 misregulation in ALS/FTLD
bioRxiv - M. Pacesa, C.-H. Lin, A. Cléry, K. Bargsten, M.J. Irby, F.H.-T. Allain, P. Cameron, P.D. Donohoue and M. Jinek (2021) Structural basis for Cas9 off-target activity
bioRxiv - M. Katsantoni, F. Gypas, C.J. Herrmann, D. Burri, M. Bak, P. Iborra, K. Agarwal, M. Ataman, A. Börsch, M. Zavolan and A. Kanitz (2021) ZARP: An automated workflow for processing of RNA-seq data
bioRxiv - M.S. Kaiser, G. Milan, S. Lin, F. Oliveri, K. Chojnowska, L.A. Tintignac, N. Mittal, C.E. Zimmerli, D.J. Glass, M. Zavolan, D.J. Ham and M.A. Rüegg (2021) Dual roles of mTORC1-dependent activation of the ubiquitin-proteasome system in muscle proteostasis
bioRxiv - S. Gómez-Puerta, R. Ferrero, T. Hochstoeger, I. Zubiri, J.A. Chao, T. Aragón and F. Voigt (2021) Live imaging of the co-translational recruitment of XBP1 mRNA to the ER and its processing by diffuse, non-polarized IRE1alpha
bioRxiv - R. Esposito, A. Lanzos, T. Polidori, H. Guillen-Ramirez, B. Merlin, L. Mela, E.o Zoni, I. Buechi, L. Hovhannisyan, F. McCluggage, M. Medo, G. Basile, D.F. Meise, S. Ramnarayanan, S. Zwyssig, C. Wenger, K. Schwarz, A. Vancura, N. Bosch-Guiteras, M. Kruithof-de Julio, Y. Zimmer, M. Medova, D. Stroka, A. Fox and R. Johnson (2021) Tumour mutations in long noncoding RNAs that enhance cell fitness
bioRxiv - M. Gultom, A. Kratzel, J. Portmann, H. Stalder, A. Chanfon Baetzner, H. Gantenbein, C. Gurtner, N. Ebert, H. Posthaus, P. Zanolari, S. Pfaender, V. Thiel and R. Dijkman (2021) Establishment of well-differentiated camelid airway cultures to study Middle East respiratory syndrome coronavirus
bioRxiv - R. Arora, M. Bodak, L. Penouty, C. Hackmann and C. Ciaudo (2021) Sequestration of LINE-1 in novel cytosolic bodies by MOV10 restricts retrotransposition
bioRxiv - R. Esposito, T. Polidori, D. Meise, C. Pulido, P. Chouvardas, S. Forster, P. Schaerer, A. Kobel, J. Schlatter, M. Roemmele, E. Westemeier, L. Zhu, A. Lanzos, H. Guillen-Ramirez, G. Basile, I. Carrozzo, A. Vancura, S. Ullrich, P. Medina, A. Andreades, D. Harvey, P. Ma, S. Haefliger, X. Wang, I. Martinez, A. Ochsenbein, C. Riether and R. Johnson (2021) Multi-hallmark long noncoding RNA maps reveal non-small cell lung cancer vulnerabilities
bioRxiv - R. Nurtdinov, M. Sanz, A. Abad, A. Esteban, S. Ullrich, C. Arnan, R. Johnson, S. Perez-Lluch and R. Guigo (2021) Alu-mediated weak CEBPA binding and slow B cell transdifferentiation in human
bioRxiv - D. Niemeyer, S. Schroeder, K. Friedmann, F. Weege, J. Trimpert, A. Richter, S. Stenzel, J. Jansen, J. Emanuel, J. Kazmierski, F. Pott, L.M. Jeworowski, R. Olmer, M.-C. Jaboreck, B. Tenner, J. Papies, J. Heinze, F. Walper, M.L. Schmidt, N. Heinemann, E. Moencke-Buchner, T. Veith, M. Baumgardt, K. Hoffmann, M. Widera, T.T.N. Thao, A. Balazs, J. Schulze, C. Mache, M. Morkel, S. Ciesek, L.G. Hanitsch, M. Mall, A.C. Hocke, V. Thiel, K. Osterrieder, T. Wolff, U. Martin, V.M. Corman, M.A. Mueller, C. Goffinet and C. Drosten (2021) Post-entry, spike-dependent replication advantage of B.1.1.7 and B.1.617.2 over B.1 SARS-CoV-2 in an ACE2-deficient human lung cell line
bioRxiv - M. Mueller, M. Schaefer, T. Faeh, D. Spies, R. Peña-Hernández, R. Santoro and C. Ciaudo (2021) ARGONAUTE proteins regulate a specific network of genes through KLF4 in mouse embryonic stem cells
bioRxiv - C.E. Dewar, S. Oeljeklaus, B. Warscheid and A. Schneider (2021) Characterisation of a highly diverged mitochondrial ATP synthase peripheral stalk subunit b in Trypanosoma brucei
bioRxiv - M. Pacesa and M. Jinek (2021) Mechanism of R-loop formation and conformational activation of Cas9
bioRxiv - C.E. Dewar, S. Oeljeklaus, J. Mani, W.W.D. Mühlhäuser, B. Warscheid and A. Schneider (2021) Mistargeting of hydrophobic mitochondrial proteins activates a nucleus-mediated posttranscriptional quality control pathway in trypanosomes
bioRxiv - A.B. Eberle, K. Schranz, S. Nasif, L. Grollmus and Oliver Mühlemann (2021) Dissecting the import and export pathways of the human RNA helicase UPF1
bioRxiv - A.J. Hume, B. Heiden, J. Olejnik, E.L. Suder, S. Ross, W.A. Scoon, E. Bullitt, M. Ericsson, M.R. White, J. Turcinovic, T.T.N. Thao, R. M. Hekman, J.E. Kaserman, J. Huang, K. Alysandratos, G.E. Toth, F. Jakab, D.N. Kotton, A.A. Wilson, A. Emili, V. Thiel, J.H. Connor, G. Kemenesi, D. Cifuentes and E. Mühlberger (2021) Recombinant Lloviu virus as a model to study inaccessible zoonotic viruses
bioRxiv - A. Brümmer, R. Dreos, A.C. Marques and S. Bergmann (2021)Analysis of eukaryotic lincRNA sequences reveals signatures of repressed translation in species under strong selection
bioRxiv - M. Roganowicz, D. Baer and R. Santoro (2021) BAZ2A-RNA mediated association with TOP2A and KDM1A represses gene expression in prostate cancer
bioRxiv - A. Kroupova, F. Ackle, F.M. Boneberg, A. Chui, S. Weitzer, M. Faini, A. Leitner, R. Aebersold, J. Martinez and M. Jinek (2021) Molecular architecture of the human tRNA ligase complex
bioRxiv - I. Querques, M. Schmitz, S. Oberli, C. Chanez and M. Jinek (2021) Molecular mechanism of target site selection and remodeling by type V CRISPR-associated transposons
bioRxiv - Y.P. Hauser, M.W.M. Meeuse, D. Gaidatzis and H. Grosshans (2021) The BLMP-1 transcription factor promotes oscillatory gene expression to achieve timely molting
bioRxiv - R. Weber, U. Ghoshdastider, D. Spies, C. Dure, F. Valdivia-Francia, M. Forny, M. Ormiston, P.F. Renz, D. Taborsky, M. Yigit, H. Yamahachi and A. Sendoel (2021) Monitoring the 5`UTR landscape reveals 5`terminal oligopyrimidine (TOP) motif switches to drive translational efficiencies
bioRxiv - M. Mueller, T. Faeh, M. Schaefer, J. Luitz, P. Stalder, R. Arora, R.P. Ngondo and C. Ciaudo (2021) AGO1 regulates major satellite transcripts and H3K9me3 distribution at pericentromeric regions in mESCs
bioRxiv - D. Burri and M. Zavolan (2021) Shortening of 3' UTRs in most cell types composing tumor tissues implicates alternative polyadenylation in protein metabolism
bioRxiv - S. Ullrich, C. Arnan, C. Pulido-Quetglass, R.N. Nurtdinov, A. Esteban, J. Blanco, E. Aparicio-Prat, R. Johnson, S. Perez-Lluch and R. Guigo (2021) Paired guide RNA CRISPR-Cas9 screening for protein-coding genes and lncRNAs involved in transdifferentiation of human B-cells to macrophages
bioRxiv - T.J. Böddeker, K.A. Rosowski, D. Berchtold, L. Emmanouilidis, Y. Han, F.H.-T. Allain, R.W. Style, L. Pelkmans and E.R. Dufresne (2021) Non-specific adhesive forces between filaments and membraneless organelles
bioRxiv - J. van den Heuvel, C. Ashiono, L. Gillet, K. Doerner, E. Wyler, I. Zemp and U. Kutay (2021) Processing of the Ribosomal Ubiquitin-Like Fusion Protein FUBI-eS30/FAU is Required for 40S Maturation and Depends on USP36
bioRxiv - K. Tabata, V. Prasad, D. Paul, J.-Y. Lee, M.-T. Pham, W.-I. Twu, C.J. Neufeldt, M. Cortese, B. Cerikan, C.S. Tran, C. Luechtenborg, P. Vkovski, K. Hoermann, A. Mueller, C. Zitzmann, U. Haselmann, J. Beneke, L. Kaderali, H. Erfle, V. Thiel, V. Lohmann, G. Superti-Furga, B. Bruegger and R. Bartenschlager (2021) Convergent use of phosphatidic acid for Hepatitis C virus and SARS-CoV-2 replication organelle formation
bioRxiv - L. Ulrich, N.J. Halwe, A. Taddeo, N. Ebert, J. Schön, C. Devisme, B.S. Trüeb, B. Hoffmann, M. Wider, M. Bekliz, M. Essaidi-Laziosi, M.L. Schmidt, D. Niemeyer, V.M. Corman, A. Kraft, A. Godel, L. Laloli, J.N. Kelly, A. Breithaupt, C. Wylezich, I.M. Berenguer Veiga, M. Gultom, K. Adea, B. Meyer, C. Eberhardt, L. Thomann, M. Gsell-Albert, F. Labroussaa, J. Jores, A. Summerfield, C. Drosten, I.A. Eckerle, R. Dijkman, D. Hoffmann, V. Thiel, M. Beer and C. Benarafa (2021) Enhanced fitness of SARS-CoV-2 variant of concern B.1.1.7, but not B.1.351, in animal models
bioRxiv - A. Iyer, M. Niemann, L. Farine, M. Serricchio, A. Schneider and P. Bütikofer (2021) The endoplasmic reticulum membrane protein complex localizes to the mitochondrial - endoplasmic reticulum interface and its subunits modulate phospholipid biosynthesis in Trypanosoma brucei
bioRxiv - P. Dave, E. Griesbach, G. Roth, D. Mateju and J. Chao (2021) Single-molecule imaging reveals the coupling of translation and mRNA decay
bioRxiv - D.J. Ham, A. Boersch, K. Chojnowska, S. Lin, A.B. Leuchtmann, A.S. Ham, M. Thuerkauf, J. Delezie, R. Furrer, D. Burri, M. Sinnreich, C. Handschin, L.A. Tintignac, M. Zavolan, N. Mittal, M.A. Ruegg (2021) Distinct and additive effects of calorie restriction and rapamycin in aging skeletal muscle
bioRxiv - L.-A. Gurzeler, J. Ziegelmuller, O. Mühlemann and E.D. Karousis (2021) Production of human translation-competent lysates using dual centrifugation
bioRxiv - R. Dijkman, M. Selvaraj, H.H. Gad, S. More, R. Hartmann, S. Perlman, V. Thiel and R. Channappanavar (2021) Effective interferon (IFN)-lambda treatment regimen to control lethal MERS-CoV infection in mice
bioRxiv - K. Tabata, V. Prasad, D. Paul, J.-Y. Lee, M.-T. Pham, W.-I. Twu, C.J. Neufeldt, M. Cortese, B. Cerikan, C.S. Tran, C. Luechtenborg, P. Vkovski, K. Hoermann, A. Mueller, C. Zitzmann, U. Haselmann, J. Beneke, L. Kaderali, H. Erfle, V. Thiel, V. Lohmann, G. Superti-Furga, B. Bruegger and R. Bartenschlager (2021) Convergent use of phosphatidic acid for Hepatitis C virus and SARS-CoV-2 replication organelle formation
bioRxiv - M. Emmenegger, E. De Cecco, M. Hruska-Plochan, T. Eninger, M.M. Schneider, M. Barth, E. Tantardini, P. de Rossi, M. Bacioglu, R.G. Langston, A. Kaganovich, N. Bengoa-Vergniory, A. Gonzalez-Guerra, M. Avar, D. Heinzer, R. Reimann, L.M. Häsler, T.W. Herling, N.S. Matharu, N. Landeck, K. Luk, R. Melki, P.J. Kahle, S. Hornemann, T.P.J. Knowles, M.R. Cookson, M. Polymenidou, M. Jucker and A. Aguzzi (2021) LAG3 is not expressed in human and murine neurons and does not modulate a-synucleinopathies
bioRxiv - E.D. Karousis, F. Gypas, M. Zavolan and O. Mühlemann (2021)Nanopore sequencing reveals endogenous NMD-targeted isoforms in human cells
bioRxiv - G. Holzer, P. De Magistris, C. Gramminger, R. Sachdev, A. Magalska, A. Schooley, A. Scheufen, B. Lennartz, M. Tatarek-Nossol, H. Lue, M.I. Linder, U. Kutay, C. Preisinger, D. Moreno-Andres and W. Antonin (2021) The nucleoporin Nup50 activates the Ran guanyl-nucleotide exchange factor RCC1 to promote mitotic NPC assembly
bioRxiv - J.A. Ruland, A.M. Krueger, K.E. Doerner, R. Bhatia, S. Wirths, D. Poetes, U. Kutay, J.P. Siebrasse and U. Kubitscheck (2021) Nuclear export of the pre-60S ribosomal subunit through single nuclear pores observed in real time
bioRxiv - M. Calon, A.A. Malar, S. Pfister, V. Rimal, M.E. Weber, T. Wiegand, J. Zehnder, M. Chavez, R. Deb, R. Cadalbert, A. Dapp, M.-L. Fogeron, A. Hunkeler, L. Lecoq, A. Torosyan, D. Zyla, R. Glockshuber, S. Jonas, M. Nassal, M. Ernst, A. Bockmann and B.H. Meier (2021) Biomolecular solid-state NMR spectroscopy at highest field: the gain in resolution at 1200 MHz
bioRxiv - T. Lenarcic, M. Jaskolowski, M. Leibundgut, A. Scaiola, T. Schoenhut, M. Saurer, R. Lee, O. Rackham, A. Filipovska and N. Ban (2021) Stepwise maturation of the peptidyl transferase region of human mitoribosomes
bioRxiv - B.D. Tobwin and H. Grosshans (2021) A folder mechanism ensures size uniformity among C. elegans individuals by coupling growth and development
bioRxiv - K.M. Hannan, P. Soo, M.S. Wong, J.K. Lee, N. Hein, M. Evers, K.D. Wysoke, T.D. Williams, C. Montellese, L. Smith, S.J. Al-Obaidi, L. Núñez-Villacís, P.a Poh, M. Pavy, J.-S. He, K.M. Parsons, J. Diesch, G. Burgio, R. Ferreira, Z.-P. Feng, C.M. Gould, P.B. Madhamshettiwar, J. Flygare, T.J. Gonda, K.J. Simpson, U. Kutay, R.B. Pearson, C. Engel, N. Watkins, R.D. Hannan and A.J. George (2021) Nuclear stabilisation of p53 requires a functional nucleolar surveillance pathway
bioRxiv - E. Kummer, K.N. Schubert, T. Schönhut, A. Scaiola and N. Ban (2021) Release, rescue and recycling: termination of translation in mammalian mitochondria
bioRxiv - F. Gruhl, P. Janich, H. Kaessmann and D. Gatfield (2021) Circular RNA repertoires are associated with evolutionarily young transposable elements
bioRxiv - A. Kratzel, J.N. Kelly, Y. Brueggemann, J. Portmann, P. V'kovski, D. Todt, N. Ebert, E. Steinmann, R. Dijkman, G. Zimmer, S. Pfaender and V. Thiel (2021) A genome-wide CRISPR screen identifies interactors of the autophagy pathway as conserved coronavirus targets
bioRxiv - M. Krepl, F. Damberger, C. von Schroetter, D. Theler, P. Pokorna, F. Allain and J. Sponer (2021) Recognition of N6-methyladenosine by the YTHDC1 YTH domain studied by molecular dynamics and NMR spectroscopy: The role of hydration
bioRxiv - S. Tetter, N. Terasaka, A. Steinauer, R.J. Bingham, S. Clark, A.P. Scott, N. Patel, M. Leibundgut, E. Wroblewski, N. Ban, P.G. Stockley, R. Twarock and D. Hilvert (2020) Evolution of a virus-like architecture and packaging mechanism in a repurposed bacterial protein
bioRxiv - O. Garcia-Nicolas, P. V'kovski, F. Zettl, G. Zimmer, V. Thiel and A. Summerfield (2020) No evidence for human monocyte-derived macrophage infection and antibody-mediated enhancement of SARS-CoV-2 infection
bioRxiv - B.Th. Eichenberger, Y.X. Zhan, M. Rempfler, L. Girogetti and J. Chao (2020) deepBlink: Threshold-independent detection and localization of diffraction-limited spots
bioRxiv - R.K. Gudipati, K. Braun, F. Gypas, D. Hess, J. Schreier, S.H. Carl, R. Ketting and H. Grosshans (2020) Protease-mediated processing of Argonaute proteins controls small RNA association
bioRxiv - B. Krasniqi, A. Stevaert, B. Van Loy, T. Nguyen, J. Thomas, J. Vandeput, D. Jochmans, V. Thiel, R. Dijkman, W. Dehaen, A. Voet and L. Naesens (2020) Betulonic acid derivatives inhibiting coronavirus replication in cell culture via the nsp15 endoribonuclease
bioRxiv - N. Luithle, J. uit de Bos, R. Hovius, D. Maslennikova, R. Lewis, R. Ungricht, B. Fierz, U. Kutay (2020) Torsin ATPases influence chromatin interaction of the Torsin regulator LAP1
bioRxiv - B. Borsari, A. Abad, C. Coimbra Klein, R. Nurtdinov, A. Esteban, E. Palumbo, M. Ruiz-Romero, M. Sanz, B.R. Correa, R. Johnson, S. Pérez-Lluch, R. Guigó (2020) Dynamics of gene expression and chromatin marking during cell state transition
bioRxiv - M. Gultom, M. Licheri, L. Laloli, M. Wider, M. Straessle, S. Steiner, A. Kratzel, T.T.N. Thao, H. Stalder, J. Portmann, M. Holwerda, P. V'kovski, N. Ebert, N. Stokar-Regenscheit, C. Gurtner, P. Zanolari, H. Posthaus, S. Schuller, A. Moreira-Soto, A. Vicente-Santos, E. Corrales-Aguilar, N. Ruggli, G. Tekes, V. von Messling, B. Sawatsky, V. Thiel, R. Dijkman (2020) Susceptibility of well-differentiated airway epithelial cell cultures from domestic and wildlife animals to SARS-CoV-2
bioRxiv - P. Simmler, C. Cortijo, L.M. Koch, P. Galliker, S. Angori, H.A. Bolck, C. Mueller, A. Vukolic, P. Mirtschink, Y. Christinat, N.R. Davidson, K.-V. Lehmann, G. Pellegrini, C. Pauli, D. Lenggenhager, I. Guccini, T. Ringel, C. Hirt, G. Raetsch, H. Moch, M. Stoffel, G. Schwank (2020) SF3B1 promotes tumor malignancy through splicing-independent co-activation of HIF1alpha
bioRxiv - B. Zhou, T.T.N. Thao, D. Hoffmann, A. Taddeo, N. Ebert, F. Labroussaa, A. Pohlmann, J. King, J. Portmann, N. J. Halwe, L. Ulrich, B.S. Trueb, J.N. Kelly, X. Fan, B. Hoffmann, S. Steiner, L. Wang, L. Thomann, X. Lin, H. Stalder, B. Pozzi, S. de Brot, N. Jiang, D. Cui, J. Hossain, M. Wilson, M.W. Keller, T.J. Stark, J.R. Barnes, R. Dijkman, J. Jores, C. Benarafa, D.E. Wentworth, V. Thiel and M. Beer (2020) SARS-CoV-2 spike D614G variant confers enhanced replication and transmissibility
bioRxiv - P.R. Bhatt, A. Scaiola, G. Loughran, M. Leibundgut, A. Kratzel, A. McMillan, K.M. O’ Connor, J.W. Bode, V. Thiel, J.F. Atkins, N. Ban (2020) Structural basis of ribosomal frameshifting during translation of the SARS-CoV-2 RNA genome
bioRxiv - L. Contu, G. Balistreri, M. Domanski, A. Uldry, O. Mühlemann (2020) Characterisation of the Semliki Forest Virus-host cell interactome reveals the viral capsid protein as an inhibitor of nonsense-mediated mRNA decay
bioRxiv - M. Linder, D. Liko, V. Kancherla, S. Piscuoglio, M.N. Hall (2020) Colitis is associated with loss of LHPP and up-regulation of histidine phosphorylation in intestinal epithelial cells
bioRxiv - N. Bakhtina, M. Muller, H. Wischnewski, R. Arora, C. Ciaudo (2020) 3D synthetic microscaffolds promote homogenous expression of NANOG in mouse embryonic stem cells
bioRxiv - L. Plassart, R. Shayan, C. Montellese, D. Rinaldi, N. Larburu, C. Pichereaux, S. Lebaron, M. O’Donohue, U. Kutay, J. Marcoux, P. Gleizes, C. Plisson-Chastang (2020) The final step of 40S ribosomal subunit maturation is controlled by a dual key lock
bioRxiv - A. Vancura, A. Lanzós, N. Bosch, M. Torres, S. Häfliger and R. Johnson (2020) Semi-automated annotation of known and novel cancer long noncoding RNAs with the Cancer LncRNA Census 2 (CLC2)
bioRxiv - N. Bosch, M. Medová, R. Esposito, C. Pulido-Quetglas, Y. Zimmer and R. Johnson (2020) Enhancing CRISPR deletion via pharmacological delay of DNA-PK
bioRxiv - P. Sharma, B.S. Nilges, J. Wu and S.A. Leidel (2019) The translation inhibitor cycloheximide affects ribosome profiling data in a species-specific manner
bioRxiv - S. Reber, H. Lindsay, A. Devoy, D. Jutzi, J. Mechtersheimer, M. Domanski, O. Mühlemann, S.M.L. Barabino and M.-D. Ruepp (2019) The phase separation-dependent FUS interactome reveals nuclear and cytoplasmic function of liquid-liquid phase separation
bioRxiv - S.C. Lenzken, B.R. Levone, G. Filosa, M. Antonaci, F. Conte, C. Kizilirmak, S. Reber, A. Loffreda, F. Biella, A.E. Ronchi, O. Mühlemann, A. Bachi, M.-D. Ruepp and S.M.L. Barabino (2019) FUS-dependent phase separation initiates double-strand break repair
bioRxiv - I. Ferro, J. Gavini, L. Bracher, M. Landolfo, D. Candinas, D. Stroka and N. Polacek (2020) The human vault RNA enhances tumorigenesis and chemoresistance through the lysosome
bioRxiv - G. Yang, C. Heisenberger, I.C. Kos-Braun, N. Polacek, J. Grillari, M. Schosserer and M. Koš1 (2020) Cellular senescence and quiescence are associated with altered ribosomal RNA methylation and processing
bioRxiv - A. Stukalov, V. Girault, V. Grass, V. Bergant, O. Karayel, C. Urban, D.A. Haas, Y. Huang, L. Oubraham, A. Wang, S.M. Hamad, A. Piras, M. Tanzer, F. M. Hansen, T. Enghleitner, M. Reinecke, T.M. Lavacca, R. Ehmann, R. Wölfel, J. Jores, B. Kuster, U. Protzer, R. Rad, J. Ziebuhr, V. Thiel, P. Scaturro, M. Mann and Andreas Pichlmair (2020) Multi-level proteomics reveals host-perturbation strategies of SARS-CoV-2 and SARS-CoV
bioRxiv - M. Holwerda, P. V’kovski, M. Wider, V. Thiel and R. Dijkman (2020) Identification of five antiviral compounds from the Pandemic Response Box targeting SARS-CoV-2
bioRxiv - P. V’kovski, M. Gultom, S. Steiner, J. Kelly, J. Russeil, B. Mangeat, E. Cora, J. Pezoldt, M. Holwerda, A. Kratzel, L. Laloli, M. Wider, J. Portmann, T. Tran, N. Ebert, H. Stalder, R. Hartmann, V. Gardeux, D. Alpern, B. Deplancke, V. Thiel and R. Dijkman (2020) Disparate temperature-dependent virus – host dynamics for SARS-CoV-2 and SARS-CoV in the human respiratory epithelium
bioRxiv - J.N. Kelly, L. Laloli, P. V’kovski, M. Holwerda, J. Portmann, V. Thiel and R. Dijkman (2020) Comprehensive single cell analysis of pandemic influenza A virus infection in the human airways uncovers cell-type specific host transcriptional signatures relevant for disease progression and pathogenesis
bioRxiv - N.S. Ravi, B. Wienert, S.K. Wyman, J. Vu, A.A. Pai, P. Balasubramanian, Y. Nakamura, R. Kurita, S. Marepally, S. Thangavel, S.R. Velayudhan, A. Srivastava, M.A. DeWitt, J.E. Corn and K.M. Mohankumar (2020) Identification of novel HPFH-like mutations by CRISPR base editing that elevates the expression of fetal hemoglobin
bioRxiv - R. Baik, S.K. Wyman, S. K. and J.E. Corn (2019) Genome editing to model and reverse a prevalent mutation associated with myeloproliferative neoplasms
bioRxiv - M.M. Duszczyk, H. Wischnewski, T. Kazeeva, F.E. Loughlin, C. von Schroetter, U. Pradère, J. Hall, C. Ciaudo and F.H.-T. Allain (2019) The solution structure of Dead End bound to AU-rich RNA reveals an unprecedented mode of tandem RRM-RNA recognition required for mRNA regulation
bioRxiv - T.C.S. Mak, Y. von Ohlen, Y. Fang Wang, E. Kane, K. Jurgaityte, P. Ervilha, P. Chabosseau, W. Distaso, V. Salem, A. Tomas, M. Stoffel, P. Marchetti, A.M.J. Shapiro, G.A. Rutter and M. Latreille (2019) B-cell dedifferentiation is associated with epithelial-mesenchymal transition triggered by miR-7-mediated repression of mSwi/Snf complex
bioRxiv - J. Scekic-Zahirovic, I. Sanjuan-Ruiz, V. Kan, S. Megat, P. De Rossi, S. Dieterlé, R. Cassel, P. Kessler, D. Wiesner, L. Tzeplaeff, V. Demais, H.-P. Muller, G. Picchiarelli, N. Mishra, S. Dirrig-Grosch, J. Kassubek, V. Rasche, A. Ludolph, A.-L. Boutillier, M. Polymenidou, C. Lagier-Tourenne, S. Liebscher and L. Dupuis (2020) Cytoplasmic accumulation of FUS triggers early behavioral alterations linked to cortical neuronal hyperactivity and defects in inhibitory synapses
bioRxiv - S. Sahadevan, K.M. Hembach, E. Tantardini, M. Pérez-Berlanga, M. Hruska-Plochan, J. Weber, P. Schwarz, L. Dupuis, M.D. Robinson, P. De Rossi and M. Polymenidou (2020) Synaptic accumulation of FUS triggers age-dependent misregulation of inhibitory synapses in ALS-FUS mice
bioRxiv - D. Mateju, B. Eichenberger, J. Eglinger, G. Roth and J.A. Chao (2020) Single-molecule imaging reveals translation of mRNAs localized to stress granules
bioRxiv - A. Scaiola, F. Mangia, S. Imseng, D. Boehringer, K. Berneiser, M. Shimobayashi, E. Stuttfeld, M.N. Hall, N. Ban and T. Maier (2020) The 3.2Å resolution structure of human mTORC2
bioRxiv - M. Shimobayashi, S. Shetty, I.C. Frei, B.K. Wölnerhanssen, D. Weissenberger, N. Dietz, A. Thomas, D. Ritz, A.C. Meyer-Gerspach, T. Maier, N. Hay, R. Peterli, N. Rohner and M.N. Hall (2020) Diet-induced loss of adipose Hexokinase 2 triggers hyperglycemia
bioRxiv - D. Benjamin, M. Colombi, C. Moroni and M.N. Hall (2019) mTOR dependent transformed human cells have a distinct set of essential genes from bcr-abl transformed cells
bioRxiv - S. Ghosh, A. Börsch and M. Zavolan (2020) The transcriptional landscape of a hepatoma cell line grown on scaffolds of extracellular matrix proteins
bioRxiv - J. Breda, M. Zavolan and E. van Nimwegen (2029) Bayesian inference of the gene expression states of single cells from scRNA-seq data
bioRxiv - C.-Y. Gabriela Lin, A.C. Näger, T. Lunardi, A. Vancevska, G. Lossaint and J. Lingner (2020) The Human Telomeric Proteome During Telomere Replication
bioRxiv - A.-S. Briod, G. Glousker and J. Lingner (2020) RADX Sustains POT1 Function at Telomeres to Counteract RAD51 Binding, which Triggers Telomere Fragility
bioRxiv - J.Y. Tan, B. Abdulkarim and A.C. Marques (2020) Noncanonical targeting contributes significantly to miRNA-mediated regulation
bioRxiv - M. Hersch, A. Biasini, A.C. Marques and S. Bergmann (2020) Estimating RNA dynamics using one time point for one sample in a single-pulse metabolic experiment
bioRxiv - A. Brümmer, R. Dreos, A.C. Marques and S. Bergmann (2020) LincRNA sequences are biased to counteract their translation
bioRxiv - A. Biasini, S. de Pretis, J.Y. Tan, B. Abdulkarim, H. Wischnewski, R. Dreos, M. Pelizzola, C. Ciaudo and A.C. Marques (2020) Translation is required for miRNA-dependent decay of endogenous transcripts
bioRxiv - D. Dalcher, J.Y., C. Bersaglieri, R. Peña-Hernández, E. Vollenweider, S. Zeyen, Ma.W. Schmid, V. Bianchi, S. Butz, R. Kuzyakiv, T. Baubec, A.C. Marques and R. Santoro (2019) TIP5 safeguards genome architecture of ground-state pluripotent stem cells
bioRxiv - R. Peña-Hernández, R. Aprigliano, S. Frommel, K. Pietrzak, S. Steiger, M. Roganowicz, J. Bizzarro and R. Santoro (2020) BAZ2A association with H3K14ac is required for the dedifferentiation of prostate cancer cells into a cancer stem-like state
bioRxiv