Disclaimer: This page includes all preprints by NCCR member labs.

Preprints

  • A. Kratzel, J.N. Kelly, Y. Brueggemann, J. Portmann, P.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
  • 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