2023
Touch receptor end-organ innervation and function requires sensory expression of the transcription factor Meis2.
Desiderio, S. and Schwaller, F. and Tartour, K. and Padmanabhan, K. and Lewin, G.R. and Carroll, P. and Marmigère, F.
bioRxiv
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6 November 2023
The synapsin-dependent vesicle cluster is crucial for presynaptic plasticity at a glutamatergic synapse in male mice.
Bruentgens, F. and Moreno Velasquez, L. and Stumpf, A. and Parthier, D. and Breustedt, J.M. and Benfenati, F. and Milovanovic, D. and Schmitz, D. and Orlando, M.
bioRxiv
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8 August 2023
Cytokines as potential novel therapeutic targets in severe inflammatory cardiomyopathy.
Suwalski, P. and Golpour, A. and Weiner, J. and Musigk, N. and Balzer, F. and Giesa, N. and Amr, A. and Trebing, J. and Sedaghat, F. and Meder, B. and Beule, D. and Landmesser, U. and Heidecker, B.
bioRxiv
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4 August 2023
RIF1 acts as a gatekeeper of B cell identity during late differentiation.
Rahjouei, A. and Kabrani, E. and Berruezo-Llacuna, M. and Altwasser, R. and Delgado-Benito, V. and Pavri, R. and Di Virgilio, M.
bioRxiv
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20 July 2023
Adjustments to the reference dataset design improves cell type label transfer.
Mölbert, C. and Haghverdi, L.
bioRxiv
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26 January 2023
Cellular and synaptic diversity of layer 2-3 pyramidal neurons in human individuals.
Planert, H. and Mittermaier, F.X. and Grosser, S. and Fidzinski, P. and Schneider, U.C. and Radbruch, H. and Onken, J. and Holtkamp, M. and Schmitz, D. and Alle, H. and Vida, I. and Geiger, J.R.P. and Peng, Y.
bioRxiv
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24 January 2023
LZTR1 polymerization provokes cardiac pathology in recessive Noonan syndrome.
Busley, A.V. and Gutiérrez-Gutiérrez, O. and Hammer, E. and Steinegger, M. and Böhmer, L. and Schroeder, H. and Kleinsorge, M. and Altmüller, J. and Marbach, F. and Hasenfuss, G. and Zimmermann, W.H. and Wollnik, B. and Cyganek, L.
bioRxiv
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10 January 2023
Prdm16 mutation determines sex-specific cardiac metabolism and identifies two novel cardiac metabolic regulators.
Kühnisch, J. and Theisen, S. and Dartsch, J. and Fritsche-Guenther, R. and Kirchner, M. and Obermayer, B. and Bauer, A. and Kahlert, A.K. and Rothe, M. and Beule, D. and Heuser, A. and Mertins, P. and Kirwan, J.A. and Berndt, N. and MacRae, C.A. and Hubner, N. and Klaassen, S.
bioRxiv
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10 January 2023
Replicative aging impedes stress-induced assembly of a key human protein disaggregase.
Mathangasinghe, Y. and Alberts, N. and Rosado, C.J. and Cox, D. and Payne, N.L. and Ormsby, A.R. and Alp, K.M. and Sakson, R. and Uthishtran, S. and Ruppert, T. and Arumugam, S. and Hatters, D.M. and Kampinga, H.H. and Nillegoda, N.B.
bioRxiv
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8 January 2023
2022
The lncRNA landscape of cardiac resident macrophages and identification of Schlafenlnc as a regulator of macrophage migratory function.
Dueck, A. and Althaus, L. and Heise, K. and Esfandyari, D. and Bayguen, S. and Brandes, R.P. and Gagneur, J. and Jae, N. and Knolle, P. and Leisegang, M.S. and Maegdefessel, L. and Meitinger, T. and Petzold, N. and Ramanujam, D. and Sager, H. and Schulz, C. and Theodorakis, E. and Uzonyi, A. and Weinberger, T. and Bader, M. and Schmidt-Supprian, M. and Engelhardt, S.
bioRxiv
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22 December 2022
Liam tackles complex multimodal single-cell data integration challenges.
Rautenstrauch, P. and Ohler, U.
bioRxiv
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22 December 2022
Differential ripple propagation along the hippocampal longitudinal axis.
de Filippo, R. and Schmitz, D.
bioRxiv
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22 December 2022
Modeling IP(3) induced Ca(2+) signaling based on its interspike interval statistics.
Friedhoff, V.N. and Falcke, M.
bioRxiv
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20 December 2022
Similar neural pathways link psychological stress and brain health in health and multiple sclerosis.
Schulz, M.A. and Hetzer, S. and Eitel, F. and Asseyer, S. and Meyer-Arndt, L. and Schmitz-Hübsch, T. and Bellmann-Strobl, J. and Cole, J.H. and Gold, S.M. and Paul, F. and Ritter, K. and Weygandt, M.
bioRxiv
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20 December 2022
Gut microbiota dysbiosis is associated with altered tryptophan metabolism and dysregulated inflammatory response in severe COVID-19.
Essex, M. and Pascual-Leone, B.M. and Löber, U. and Kuhring, M. and Zhang, B. and Bruening, U. and Fritsche-Guenther, R. and Krzanowski, M. and Vernengo, F.F. and Brumhard, S. and Röwekamp, I. and Bielecka, A.A. and Lesker, T.R. and Wyler, E. and Landthaler, M. and Mantei, A. and Meisel, C. and Caesar, S. and Thiebeault, C. and Corman, V. and Marko, L. and Suttorp, N. and Strowig, T. and Kurth, F. and Sander, L.E. and Li, Y. and Kirwan, J.A. and Forslund, S.K. and Opitz, B.
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The rate of spontaneous mutations in yeast deficient for MutSβ function.
Plavskin, Y. and de Biase, M.S. and Schwarz, R.F. and Siegal, M.L.
bioRxiv
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26 November 2022
Expanding the Huntington’s disease research toolbox; validated subdomain protein constructs for biochemical and structural investigation of huntingtin.
Alteen, M.G. and Deme, J.C. and Alvarez, C.P. and Loppnau, P. and Hutchinson, A. and Seitova, A. and Chandrasekaran, R. and Silva Ramos, E. and Secker, C. and Alqazzaz, M. and Wanker, E.E. and Lea, S.M. and Arrowsmith, C.H. and Harding, R.J.
bioRxiv
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22 November 2022
Therapy-induced senescence upregulates antigen presentation machinery and triggers anti-tumor immunity in Acute Myeloid Leukemia.
Gilioli, D. and Fusco, S. and Tavella, T. and Giannetti, K. and Conti, A. and Santoro, A. and Carsana, E. and Beretta, S. and Schönlein, M. and Gambacorta, V. and Aletti, F.M. and Carraba, M.G. and Bonini, C. and Ciceri, F. and Merelli, I. and Vago, L. and Schmitt, C.A. and Di Micco, R.
bioRxiv
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17 November 2022
The molecular mechanism and physiological role of silent nociceptor activation.
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bioRxiv
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19 October 2022
Branch point evolution controls species-specific alternative splicing and regulates long term potentiation.
Franz, A. and Weber, A.I. and Preußner, M. and Dimos, N. and Stumpf, A. and Ji, Y. and Moreno-Velasquez, L. and Voigt, A. and Schulz, F. and Neumann, A. and Kuropka, B. and Kühn, R. and Urlaub, H. and Schmitz, D. and Wahl, M.C. and Heyd, F.
bioRxiv
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11 September 2022
Regulation of prostate androgens by megalin and 25-hydroxyvitamin D status: Mechanism for high prostate androgen in African American men.
Garcia, J. and Krieger, K. and Loitz, C. and Perez, L.M. and Richards, Z.A. and Helou, Y.B. and Kregel, S. and Selada, S. and Mesaros, C.A. and Gann, P. and Willnow, T.E. and Vander Griend, D. and Kittles, R. and Prins, G. and Penning, T. and Nonn, L.
bioRxiv
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1 September 2022
Coordinated cadherin functions sculpt respiratory motor circuit connectivity.
Vagnozzi, A.N. and Moore, M.T. and Lin, M. and Brozost, E.M. and KC, R. and Agarwal, A. and Schwarz, L.A. and Duan, X. and Zampieri, N. and Landmesser, L.T. and Philippidou, P.
bioRxiv
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4 August 2022
SMITH: spatially constrained stochastic model for simulation of intra-tumour heterogeneity.
Streck, A. and Kaufmann, T. and Schwarz, R.F.
bioRxiv
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24 July 2022
Npl3 functions in mRNP assembly by recruitment of mRNP components to the transcription site and their transfer onto the mRNA.
Keil, P. and Wulf, A. and Kachariya, N. and Reuscher, S. and Hühn, K. and Silbern, I. and Altmüller, J. and Stehle, R. and Zarnack, K. and Sattler, M. and Urlaub, H. and Sträßer, K.
bioRxiv
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22 July 2022
Monitoring mitochondrial translation by pulse SILAC.
Imami, K. and Selbach, M. and Ishihama, Y.
bioRxiv
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8 June 2022
Long-term imaging reveals behavioral plasticity during C. elegans dauer exit.
Preusser, F. and Neuschulz, A. and Junker, J.P. and Rajewsky, N. and Preibisch, S.
bioRxiv
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26 April 2022
The little skate genome and the evolutionary emergence of wing-like fin appendages.
Marletaz, F. and de la Calle-Mustienes, E. and Acemel, R.D. and Nakamura, T. and Paliou, C. and Naranjo, S. and Martinez-Garcia, P.M. and Cases, I. and Sleight, V.A. and Hirschberger, C. and Marcet-Houben, M. and Navon, D. and Andrescavage, A. and Skvortsova, K. and Duckett, P.E. and Gonzalez-Rajal, A. and Bogdanovic, O. and Gibcus, J.H. and Yang, L. and Gallardo-Fuentes, L. and Sospedra, I. and Lopez-Rios, J. and Darbellay, F. and Visel, A. and Dekker, J. and Shubin, N. and Gabaldon, T. and Tena, J.J. and Lupianez, D.G. and Rokhsar, D.S. and Gomez-Skarmeta, J.L.
bioRxiv
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22 March 2022
Global analysis of human-to-mouse contact-dependent intercellular mRNA and lncRNA transfer in cell culture.
Dasgupta, Sandipan and Dyagi, Daniella Y. and Haimovich, Gal and Wyler, E. and Olender, Tsviya and Singer, Robert H. and Landthaler, M. and Gerst, Jeffrey E
bioRxiv
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7 March 2022
Despite the odds: formation of the SARS-CoV-2 methylation complex.
Matsuda, A. and Plewka, J. and Chykunova, Y. and Jones, A.N. and Pachota, M. and Rawski, M. and Mourão, A. and Karim, A. and Kresik, L. and Lis, K. and Minia, I. and Hartman, K. and Sonani, R. and Schlauderer, F. and Dubin, G. and Sattler, M. and Suder, P. and Popowicz, G. and Pyrć, K. and Czarna, A.
bioRxiv
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1 March 2022
Aging-regulated TUG1 is dispensable for endothelial cell function.
Gimbel, A.T. and Koziarek, S. and Theodorou, K. and Schulz, J.F. and Stanicek, L. and Ali, T. and Günther, S. and Kumar, S. and Jo, H. and Hübner, N. and Maegdefessel, L. and Dimmeler, S. and van Heesch, S. and Boon, R.A.
bioRxiv
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28 February 2022
The SPOC domain is a phosphoserine binding module that bridges transcription machinery with co- and post-transcriptional regulators.
Appel, L.M. and Grishkovskaya, I. and Benedum, J. and Franke, V. and Polyansky, A. and Neudolt, A. and Wunder, A. and Zagrovic, B. and Akalin, A. and Djinovic-Carugo, K. and Slade, D.
bioRxiv
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27 February 2022
One gene - two proteins: the C-terminus of the prototypical M2 muscarinic receptor localizes to the mitochondria.
Fasciani, I. and Petragnano, F. and Wang, Z. and Edwards, R. and Telugu, N. and Pietrantoni, I. and Zauber, H. and Rossi, M. and Zabel, U. and Grieben, M. and Terzenidou, M.E. and Di Gregorio, J. and Pellegrini, C. and Santini, S. and Taddei, A.R. and Poehl, B. and Aringhieri, S. and Aloisi, G. and Marampon, F. and Roman, A. and Diecke, S. and Flati, V. and Giorgi, F. and Amicarelli, F. and Tobin, A.B. and Scarselli, M. and Tokatlidis, K. and Lohse, M.J. and Maggio, R. and Annibale, P.
bioRxiv
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26 February 2022
C. difficile is overdiagnosed in adults and a commensal in infants.
Ferretti, P. and Wirbel, J. and Maistrenko, O.M. and Van Rossum, T. and Alves, R. and Fullam, A. and Akanni, W. and Schudoma, C. and Schwarz, A. and Thielemann, R. and Thomas, L. and Kuhn, M. and Zeller, G. and Schmidt, T.S.B. and Bork, P.
bioRxiv
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18 February 2022
PyZebraScope: an open-source platform for brain-wide neural activity imaging in zebrafish.
Barbara, R. and Nagathihalli Kantharaju, M. and Haruvi, R. and Harrington, K. and Kawashima, T.
bioRxiv
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15 February 2022
Spatio-temporal, optogenetic control of gene expression in organoids.
Legnini, I. and Emmenegger, L. and Zappulo, A. and Wurmus, R. and Oliveras Martinez, A. and Cerda Jara, C. and Boltengagen, A. and Hessler, T. and Mastrobuoni, G. and Rybak-Wolf, A. and Kempa, S. and Zinzen, R.P. and Woehler, A. and Rajewsky, N.
bioRxiv
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9 February 2022
A single-cell atlas of de novo β-cell regeneration reveals the contribution of hybrid β/δ cells to diabetes recovery in zebrafish.
Singh, S.P. and Chawla, P. and Hnatiuk, A. and Kamel, M. and Silva, L.D. and Spanjard, B. and Eski, S.E. and Janjuha, S. and Olivares, P. and Kayisoglu, O. and Rost, F. and Bläsche, J. and Kränkel, A. and Petzold, A. and Kurth, T. and Reinhardt, S. and Junker, J.P. and Ninov, N.
bioRxiv
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31 January 2022
Functional and evolutionary significance of unknown genes from uncultivated taxa.
Rodríguez del Río, Á. and Giner-Lamia, J. and Cantalapiedra, C.P. and Botas, J. and Deng, Z. and Hernández-Plaza, A. and Paoli, L. and Schmidt, T.S.B. and Sunagawa, S. and Bork, P. and Coelho, L.P. and Huerta-Cepas, J.
bioRxiv
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27 January 2022
Identifying interpretable gene-biomarker associations with functionally informed kernel-based tests in 190,000 exomes.
Monti, R. and Rautenstrauch, P. and Ghanbari, M. and James, A.R. and Ohler, U. and Konigorski, S. and Lippert, C.
bioRxiv
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20 January 2022
Proteolytic cleavage of the extracellular domain affects signaling of parathyroid hormone receptor 1.
Klenk, C. and Hommers, L. and Lohse, M.J.
bioRxiv
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19 January 2022
2021
The single-cell transcriptional landscape of lung carcinoid tumors.
Bischoff, P. and Trinks, A. and Wiederspahn, J. and Obermayer, B. and Pett, J.P. and Jurmeister, P. and Elsner, A. and Dziodzio, T. and Rückert, J.C. and Neudecker, J. and Falk, C. and Beule, D. and Sers, C. and Morkel, M. and Horst, D. and Klauschen, F. and Blüthgen, N.
bioRxiv
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8 December 2021
Diverse but unique astrocytic phenotypes during embryonic stem cell differentiation, culturing and aging.
Freitag, K. and Eede, P. and Ivanov, A. and Schneeberger, S. and Borodina, T. and Sauer, S. and Beule, D. and Heppner, F.L.
bioRxiv
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28 November 2021
Rapid nuclear deadenylation of mammalian messenger RNA.
Alles, J. and Legnini, I. and Pacelli, M. and Rajewsky, N.
bioRxiv
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18 November 2021
Urbanization promotes specific bacteria in freshwater microbiomes including potential pathogens.
Numberger, D. and Zoccarato, L. and Woodhouse, J. and Ganzert, L. and Sauer, S. and Grossart, H.P. and Greenwood, A.D.
bioRxiv
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8 November 2021
RS-FISH: Precise, interactive, fast, and scalable FISH spot detection.
Bahry, E. and Breimann, L. and Zouinkhi, M. and Epstein, L. and Kolyvanov, K. and Long, X. and Harrington, K.I.S. and Lionnet, T. and Preibisch, S.
bioRxiv
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18 October 2021
On the relation between input and output distributions of scRNA-seq experiments.
Schwabe, D. and Falcke, M.
bioRxiv
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9 October 2021
Drivers and determinants of strain dynamics following faecal microbiota transplantation.
Schmidt, T.S.B. and Li, S.S. and Maistrenko, O.M. and Akanni, W. and Coelho, L.P. and Dolai, S. and Fullam, A. and Glazek, A.M. and Hercog, R. and Herrema, H. and Jung, F. and Kandels, S. and Orakov, A. and Van Rossum, T. and Benes, V. and Borody, T.J. and de Vos, W.M. and Ponsioen, C.Y. and Nieuwdorp, M. and Bork, P.
bioRxiv
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30 September 2021
The H4K20 demethylase DPY-21 regulates the dynamics of condensin DC binding.
Breimann, L. and Morao, A.K. and Kim, J. and Jimenez, D. and Maryn, N. and Bikkasani, K. and Carrozza, M.J. and Albritton, S.E. and Kramer, M. and Street, L.A. and Cerimi, K. and Schumann, V.F. and Bahry, E. and Preibisch, S. and Woehler, A. and Ercan, S.
bioRxiv
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24 September 2021
Dual-color fluorescence cross-correlation spectroscopy to study protein-protein interaction and protein dynamics in live cells.
Hemmen, K. and Choudhury, S. and Friedrich, M. and Balkenhol, J. and Knote, F. and Lohse, M. and Heinze, K.G.
bioRxiv
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12 September 2021
MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution.
Kaufmann, T.L. and Petkovic, M. and Watkins, T.B.K. and Colliver, E.C. and Laskina, S. and Thapa, N. and Minussi, D.C. and Navin, N. and Swanton, C. and Van Loo, P. and Haase, K. and Tarabichi, M. and Schwarz, R.F.
bioRxiv
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6 September 2021
Single-cell proteo-genomic reference maps of the hematopoietic system enable the purification and massive profiling of precisely defined cell states.
Triana, S.H. and Vonficht, D. and Jopp-Saile, L. and Raffel, S. and Lutz, R. and Leonce, D. and Ordoñez-Rueda, D. and Ramasz, B. and Boch, T. and Jann, J.C. and Nowak, D. and Hofmann, W.K. and Müller-Tidow, C. and Hübschmann, D. and Alexandrov, T. and Benes, V. and Trumpp, A. and Paulsen, M. and Velten, L. and Haas, S.
bioRxiv
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2 September 2021
Exon junction complex-associated multi-adapter RNPS1 nucleates splicing regulatory complexes to maintain transcriptome surveillance.
Schlautmann, L.P. and Boehm, V. and Lackmann, J.W. and Altmüller, J. and Dieterich, C. and Gehring, N.H.
bioRxiv
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20 August 2021
Immune competence and spleen size scale with colony status in the naked mole-rat.
Bégay, V. and Cirovic, B. and Barker, A.J. and Klopfleisch, R. and Hart, D.W. and Bennett, N.C. and Lewin, G.R.
bioRxiv
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15 August 2021
Automated reconstruction of whole-embryo cell lineages by learning from sparse annotations.
Malin-Mayor, C. and Hirsch, P. and Guignard, L. and McDole, K. and Wan, Y. and Lemon, W.C. and Keller, P.J. and Preibisch, S. and Funke, J.
bioRxiv
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29 July 2021
PatchPerPixMatch for automated 3d search of neuronal morphologies in light microscopy.
Mais, L. and Hirsch, P. and Managan, C. and Wang, K. and Rokicki, K. and Svirskas, R.R. and Dickson, B.J. and Korff, W. and Rubin, G.M. and Ihrke, G. and Meissner, G.W. and Kainmueller, D.
bioRxiv
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26 July 2021
Engineering, decoding and systems-level characterization of chimpanzee cytomegalovirus.
Phan, Q.V. and Bogdanow, B. and Wyler, E. and Landthaler, M. and Liu, F. and Hagemeier, C. and Wiebusch, L.
bioRxiv
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20 July 2021
UPF3A and UPF3B are redundant and modular activators of nonsense-mediated mRNA decay in human cells.
Wallmeroth, D. and Boehm, V. and Lackmann, J.W. and Altmüller, J. and Dieterich, C. and Gehring, N.H.
bioRxiv
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13 July 2021
Proteome-wide quantitative RNA interactome capture (qRIC) identifies phosphorylation sites with regulatory potential in RBM20.
Vieira-Vieira, C.H. and Dauksaite, V. and Gotthardt, M. and Selbach, M.
bioRxiv
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12 July 2021
Multifunctional RNA-binding proteins influence mRNA abundance and translational efficiency of distinct sets of target genes.
Schneider-Lunitz, V. and Ruiz-Orera, J. and Hubner, N. and van Heesch, S.
bioRxiv
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6 July 2021
The Cl(-)-channel TMEM16A controls the generation of cochlear Ca(2+) waves and promotes the refinement of auditory brainstem networks.
Maul, A. and Jovanovic, S. and Huebner, A.K. and Strenzke, N. and Moser, T. and Rübsamen, R. and Hübner, C.A.
bioRxiv
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5 July 2021
An executive center for the intake of liquids.
Dempsey, B. and Sungeelee, S. and Bokiniec, P. and Chettouh, Z. and Diem, S. and Autran, S. and Harrell, E.R. and Poulet, J.F.A. and Birchmeier, C. and Carrey, H. and Genovesio, A. and McMullan, S. and Goridis, C. and Fortin, G. and Brunet, J.F.
bioRxiv
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4 July 2021
Insulin mRNA is stored in RNA granules in resting beta cells.
Vasiljević, J. and Vasiljević, D. and Ganß, K. and Sönmez, A. and Wegbrod, C. and Quezada, E. and Münster, C. and Schöniger, E. and Friedland, D. and Kipke, N. and Distler, M. and Selbach, M. and Solimena, M.
bioRxiv
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29 June 2021
Timed global reorganization of protein synthesis during neocortex neurogenesis at codon resolution.
Harnett, D. and Ambrozkiewicz, M.C. and Zinnall, U. and Borisova, E. and Rusanova, A. and Dannenberg, R. and Imami, K. and Münster-Wandowski, A. and Fauler, B. and Mielke, T. and Selbach, M. and Landthaler, M. and Spahn, C.M.T. and Tarabykin, V. and Ohler, U. and Kraushar, M.L.
bioRxiv
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24 June 2021
Novel LOTUS-domain proteins are organizational hubs that recruit C. elegans Vasa to germ granules.
Cipriani, P.G. and Bay, O. and Zinno, J.P. and Gutwein, M. and Gan, H.H. and Mayya, V. and Chung, G. and Chen, J.X. and Fahs, H. and Guan, Y. and Duchaine, T. and Selbach, M. and Piano, F. and Gunsalus, K.
bioRxiv
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17 June 2021
Neuroblastoma signalling models unveil combination therapies targeting feedback-mediated resistance.
Dorel, M. and Klinger, B. and Mari, T. and Toedling, J. and Blanc, E. and Messerschmidt, C. and Nadler-Holly, M. and Ziehm, M. and Sieber, A. and Hertwig, F. and Beule, D. and Eggert, A. and Schulte, J.H. and Selbach, M. and Blüthgen, N.
bioRxiv
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14 June 2021
Principles of ecDNA random inheritance drive rapid genome change and therapy resistance in human cancers.
Lange, J.T. and Chen, C.Y. and Pichugin, Y. and Xie, L. and Tang, J. and Hung, K.L. and Yost, K.E. and Shi, Q. and Erb, M.L. and Rajkumar, U. and Wu, S. and Swanton, C. and Liu, Z. and Huang, W. and Chang, H.Y. and Bafna, V. and Henssen, A.G. and Werner, B. and Mischel, P.S.
bioRxiv
: 10.1101/2021.06.11.447968.
11 June 2021
Emerging single cell endothelial heterogeneity supports sprouting tumour angiogenesis and growth.
Matsumoto, K. and Rambow, F. and Stanchi, F. and Mathivet, T. and Qian, J. and Giese, W. and He, L. and Lambrechts, D. and Zhou, B. and Betsholtz, C. and Marine, J.C. and Gerhardt, H.
bioRxiv
: 2021.06.09.447719.
11 June 2021
Single-cell transcriptomic analysis of antiviral responses and viral antagonism in Chikungunya virus-infected synovial fibroblasts.
Pott, F. and Postmus, D. and Brown, R.J.P. and Wyler, E. and Neumann, E. and Landthaler, M. and Goffinet, C.
bioRxiv
: 2020.06.07.138610.
11 June 2021
A community-driven roadmap to advance research on translated open reading frames detected by Ribo-seq.
Mudge, J.M. and Ruiz-Orera, J. and Prensner, J.R. and Brunet, M.A. and Gonzalez, J.M. and Magrane, M. and Martinez, T. and Schulz, J.F. and Yang, Y.T. and Albà, M.M. and Baranov, P.V. and Bazzini, A. and Bruford, E. and Martin, M.J. and Carvunis, A.R. and Chen, J. and Couso, J.P. and Flicek, P. and Frankish, A. and Gerstein, M. and Hubner, N. and Ingolia, N.T. and Menschaert, G. and Ohler, U. and Roucou, X. and Saghatelian, A. and Weissman, J. and van Heesch, S.
bioRxiv
: 2021.06.10.447896.
10 June 2021
Assessing genome-wide dynamic changes in enhancer activity during early mESC differentiation by FAIRE-STARR-seq.
Glaser, L.V. and Steiger, M. and Fuchs, A. and van Bömmel, A. and Einfeldt, E. and Chung, H.R. and Vingron, M. and Meijsing, S.H.
bioRxiv
: 2021.06.04.446899.
6 June 2021
Investigating the concept of accessibility for predicting novel RNA-RNA interactions.
Reißer, S. and Meyer, I.M.
bioRxiv
: 2021.06.03.446902.
3 June 2021
Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data.
Dimchev, G. and Amiri, B. and Fäßler, F. and Falcke, M. and Schur, F.K.M.
bioRxiv
: 2021.05.25.445599.
25 May 2021
ApoE4 disrupts interaction of sortilin with fatty acid-binding protein 7 essential to promote lipid signaling.
Asaro, A. and Sinha, R. and Bakun, M. and Kalnytska, O. and Carlo-Spiewok, A.S. and Rubel, T. and Rozeboom, A. and Dadlez, M. and Kaminska, B. and Aronica, E. and Malik, A.R. and Willnow, T.E.
bioRxiv
: 2021.05.20.444938.
20 May 2021
PiggyBac transposable element-derived 1 controls neuronal progenitor identity, stress sensing and mammal-specific paraspeckles.
Raskó, T. and Pande, A. and Radscheit, K. and Zink, A. and Singh, M. and Sommer, C. and Wachtl, G. and Kolacsek, O. and Inak, G. and Szvetnik, A. and Petrakis, S. and Bunse, M. and Bansal, V. and Selbach, M. and Orbán, T. and Prigione, A. and Hurst, L.D. and Izsvák, Z.
bioRxiv
: 2021.05.19.444448.
19 May 2021
Disrupting the CD177:proteinase 3 membrane complex reduces anti-PR3 antibody-induced neutrophil activation.
Marino, S.F. and Jerke, U. and Rolle, S. and Daumke, O. and Kettritz, R.
bioRxiv
: 2021.05.17.444335.
17 May 2021
Simultaneous dimensionality reduction and integration for single-cell ATAC-seq data using deep learning.
Kopp, W. and Akalin, A. and Ohler, U.
bioRxiv
: 2021.05.11.443540.
12 May 2021
Cell-type specialization in the brain is encoded by specific long-range chromatin topologies.
Winick-Ng, W. and Kukalev, A. and Harabula, I. and Zea Redondo, L. and Meijer, M. and Serebreni, L. and Bianco, S. and Szabo, D. and Chiariello, A.M. and Irastorza-Azcarate, I. and Fiorillo, L. and Musella, F. and Thieme, C. and Irani, E. and Torlai Triglia, E. and Kolodziejczyk, A.A. and Abentung, A. and Apostolova, G, and Paul, E.J. and Franke, V. and Kempfer, R. and Akalin, A. and Teichmann, S. and Dechant, G. and Ungless, M.A. and Nicodemi, M. and Castelo-Branco, G. and Pombo, A.
bioRxiv
: 2020.04.02.020990.
12 May 2021
CYCLeR - a novel tool for the full isoform assembly and quantification of circRNAs.
Stefanov, S.R. and Meyer, I.M.
bioRxiv
: 2021.04.27.441578.
28 April 2021
The neuroinflammatory interleukin-12 signaling pathway drives Alzheimer's disease-like pathology by perturbing oligodendrocyte survival and neuronal homeostasis.
Schneeberger, S. and Kim, S.J. and Eede, P. and Boltengagen, A. and Braeuning, C. and Andreadou, M. and Becher, B. and Karaiskos, N. and Kocks, C. and Rajewsky, N. and Heppner, F.L.
bioRxiv
: 2021.04.25.441313.
27 April 2021
The SEQC2 Epigenomics Quality Control (EpiQC) Study: comprehensive characterization of epigenetic methods, reproducibility, and quantification.
Foox, J. and Nordlund, J. and Lalancette, C. and Gong, T. and Lacey, M. and Lent, S. and Langhorst, B.W. and Ponnaluri, V.K.C. and Williams, L. and Padmamabhan, K. and Cavalcante, R. and Lundmark, A. and Butler, D. and Gurvitch, J. and Greally, J.M. and Suzuki, M. and Menor, M. and Nasu, M. and Alonso, A. and Sheridan, C. and Scherer, A. and Bruinsma, S. and Golda, G. and Muszynska, A. and Labaj, P.P. and Campbe, M.A. and Wos, F. and Raine, A. and Liljedahl, U. and Axelsson, T. and Wang, C. and Chen, Z. and Yang, Z. and Li, J. and Yang, X. and Wang, H. and Melnick, A. and Guo, S. and Blume, A. and Franke, V. and Ibanez de Caceres, I. and Rodriguez-Antolin, C. and Rosas, R. and Wade Davis, J. and Ishii, J. and Megherbi, D.B. and Xiao, W. and Liao, W. and Xu, J. and Hong, H. and Ning, B. and Tong, W. and Akalin, A. and Wang, Y. and Wang, Y. and Mason, C.E.
bioRxiv
: 2020.12.14.421529.
26 April 2021
In vivo dissection of a clustered-CTCF domain boundary reveals developmental principles of regulatory insulation.
Anania, C. and Acemel, R.D. and Jedamzick, J. and Bolondi, A. and Cova, G. and Brieske, N. and Kuehn, R. and Wittler, L. and Real, F.M. and Lupianez, D.G.
bioRxiv
: 2021.04.14.439779.
14 April 2021
Dual-function RNA-binding proteins influence mRNA abundance and translational efficiency of distinct sets of target genes.
Schneider-Lunitz, V. and Ruiz-Orera, J. and Hubner, N. and van Heesch, S.
bioRxiv
: 2021.04.13.439465.
13 April 2021
Aging affects K(V)7 channels and perivascular-adipose tissue-mediated vascular tone.
Wang, Y. and Yildiz, F. and Struve, A. and Kassmann, M. and Luft, F. and Gollasch, M. and Tsvetkov, D.
bioRxiv
: 2021.04.11.438975.
11 April 2021
Expression of a modified astrocytic glutamate transporter alleviates Huntington’s hypokinesia, promotes synaptic glutamate clearance and counteracts potentially adverse EAAT2 interactions.
Hirschberg, S. and Dvorzhak, A. and Rasooli-Nejad, S.M.A. and Angelov, S. and Kirchner, M. and Mertins, P. and Lättig-Tünnemann, G. and Harms, C. and Schmitz, D. and Grantyn, R.
bioRxiv
: 2020.09.17.302158.
26 March 2021
Somatostatin interneurons activated by 5-HT2A receptor suppress slow oscillations in medial entorhinal cortex.
de Filippo, R. and Rost, B.R. and Stumpf, A. and Cooper, C. and Tukker, J.J. and Harms, C. and Beed, P. and Schmitz, D.
bioRxiv
: 2020.05.26.113373.
25 March 2021
Uncharted biosynthetic potential of the ocean microbiome.
Paoli, L. and Ruscheweyh, H.J. and Forneris, C.C. and Kautsar, S. and Clayssen, Q. and Salazar, G. and Milanese, A. and Gehrig, D. and Larralde, M. and Carroll, L.M. and Sánchez, P. and Zayed, A.A. and Cronin, D.R. and Acinas, S.G. and Bork, P. and Bowler, C. and Delmont, T.O. and Sullivan, M.B. and Wincker, P. and Zeller, G. and Robinson, S.L. and Piel, J. and Sunagawa, S.
bioRxiv
: 2021.03.24.436479.
24 March 2021
Herpesviral induction of germline transcription factor DUX4 is critical for viral gene expression.
Walter, S. and Franke, V. and Drayman, N. and Wyler, E. and Tay, S. and Landthaler, M. and Akalin, A. and Ensser, A. and Full, F.
bioRxiv
: 2021.03.24.436599.
24 March 2021
N-myristoyltransferase inhibition is synthetic lethal in MYC-deregulated cancers.
Lueg, G.A. and Faronato, M. and Gorelik, A. and Grocin, A.G. and Caamano-Gutierrez, E. and Falciani, F. and Solari, R. and Carr, R. and Bell, A.S. and Bartlett, E. and Hutton, J.A. and Llorian-Sopena, M. and Chakravarty, P. and Brzezicha, B. and Janz, M. and Garnett, M.J. and Calado, D.P. and Tate, E.W.
bioRxiv
: 2021.03.20.436222.
20 March 2021
Svep1 stabilizes developmental vascular anastomosis in reduced flow conditions.
Coxam, B. and Padberg, Y. and Maier, K. and Jung, S. and Bartels-Klein, E. and Szymborska, A. and Finotto, L. and Schulte-Merker, S. and Gerhardt, H.
bioRxiv
: 2021.03.13.435246.
19 March 2021
Complex population dynamics in a spatial microbial ecosystem with Physarum polycephalum.
Epstein, L. and Dubois, Z. and Smith, J. and Lee, Y. and Harrington, K.
bioRxiv
: 2021.03.14.435300.
15 March 2021
Mitochondrial variant enrichment from high-throughput single-cell RNA-seq resolves clonal populations.
Miller, T.E. and Lareau, C.A. and Verga, J.A. and Ssozi, D. and Ludwig, L.S. and El Farran, C. and Griffin, G.K. and Lane, A.A. and Bernstein, B.E. and Sankaran, V.G. and van Galen, P.
bioRxiv
: 2021.03.08.434450.
9 March 2021
Neurodegeneration in human brain organoids infected with herpes simplex virus type 1.
Rybak-Wolf, A. and Wyler, E. and Legnini, I. and Loewa, A. and Glažar, P. and Kim, S.J. and Pentimalli, T.M. and Oliveras Martinez, A. and Beyersdorf, B. and Woehler, A. and Landthaler, M. and Rajewsky, N.
bioRxiv
: 2021.03.05.434122.
7 March 2021
Optogenetic silencing of neurotransmitter release with a naturally occurring invertebrate rhodopsin.
Mahn, M. and Saraf-Sinik, I. and Patil, P. and Pulin, M. and Bitton, E. and Karalis, N. and Bruentgens, F. and Palgi, S. and Gat, A. and Dine, J. and Wietek, J. and Davidi, I. and Levy, R. and Litvin, A. and Zhou, F. and Sauter, K. and Soba, P. and Schmitz, D. and Luthi, A. and Rost, B.R. and Wiegert, J.S. and Yizhar, O.
bioRxiv
: 2021.02.18.431673.
18 February 2021
SUMOylation of the chromodomain factor MRG-1 in C. elegans affects chromatin-regulatory dynamics.
Baytek, G. and Blume, A. and Gerceker Demirel, F. and Bulut, S. and Mertins, P. and Tursun, B.
bioRxiv
: 2021.02.14.431134.
14 February 2021
Fast, efficient and virus-free generation of TRAC-replaced CAR T cells.
Kath, J. and Du, W. and Thommandru, B. and Turk, R. and Amini, L. and Stein, M. and Zittel, T. and Martini, S. and Ostendorf, L. and Wilhelm, A. and Akyuez, L. and Rehm, A. and Hoepken, U.E. and Pruss, A. and Kuenkele, A. and Jacobi, A.M. and Volk, H.D. and Schmueck-Henneresse, M. and Reinke, P. and Wagner, D.L.
bioRxiv
: 2021.02.14.431017.
14 February 2021
Rabies anterograde monosynaptic tracing reveals organization of spinal sensory circuits.
Pimpinella, S. and Zampieri, N.
bioRxiv
: 429920.
11 February 2021
On the distribution of spinal premotor interneurons.
Ronzano, R. and Skarlatou, S. and Bannatyne, B.A. and Bhumbra, G.S. and Foster, J.D. and Lancelin, C. and Pocratsky, A. and Ozyurt, M.G. and Smith, C.C. and Todd, A.J. and Maxwell, D.J. and Murray, A.J. and Brownstone, R.M. and Zampieri, N. and Beato, M.
bioRxiv
: 2021.02.10.430608.
11 February 2021
Differences in interactions between transmembrane domains tune the activation of metabotropic glutamate receptors.
Thibado, J. and Tano, J.Y. and Lee, J. and Salas-Estrada, L. and Provasi, D. and Strauss, A. and Lamim Ribeiro, J.M. and Xiang, G. and Broichhagen, J. and Filizola, M. and Lohse, M. and Levitz, J.
bioRxiv
: 2021.02.04.429701.
6 February 2021
Protective immune trajectories in early viral containment of non-pneumonic SARS-CoV-2 infection.
Pekayvaz, K. and Leunig, A. and Kaiser, R. and Brambs, S. and Joppich, M. and Janjic, A. and Popp, O. and Polewka, V. and Wange, L.E. and Gold, C. and Kirchner, M. and Muenchhoff, M. and Hellmuth, J.C. and Scherer, C. and Eser, T. and Deák, F. and Kuhl, N. and Linder, A. and Saar, K. and Tomas, L. and Schulz, C. and Enard, W. and Kroidl, I. and Geldmacher, C. and von Bergwelt-Baildon, M. and Keppler, O.T. and Zimmer, R. and Mertins, P. and Hubner, N. and Hölscher, M. and Massberg, S. and Stark, K. and Nicolai, L.
bioRxiv
: 2021.02.03.429351.
3 February 2021
AI-driven Deep Visual Proteomics defines cell identity and heterogeneity.
Mund, A. and Coscia, F. and Hollandi, R. and Kovács, F. and Kriston, A. and Brunner, A.D. and Bzorek, M. and Naimy, S. and Rahbek Gjerdrum, L.M. and Dyring-Andersen, B. and Bulkescher, J. and Lukas, C. and Gnann, C. and Lundberg, E. and Horvath, P. and Mann, M.
bioRxiv
: 2021.01.25.427969.
27 January 2021
Cellular drivers of injury response and regeneration in the adult zebrafish heart.
Hu, B. and Lelek, S. and Spanjaard, B. and Simões, M.G. and Aliee, H. and Schäfer, R. and Theis, F. and Panáková, D. and Junker, J.P.
bioRxiv
: 2021.01.07.425670.
7 January 2021
2020
Sox2 levels configure the WNT response of epiblast progenitors responsible for vertebrate body formation.
Blassberg, R. and Patel, H. and Watson, T. and Gouti, M. and Metzis, V. and Delás, M.J. and Briscoe, J.
bioRxiv
: 2020.12.29.424684.
30 December 2020
A comprehensive motifs-based interactome of the C/EBPα transcription factor.
Ramberger, E. and Sapozhnikova, V. and Kowenz-Leutz, E. and Zimmermann, K. and Nicot, N. and Nazarov, P.V. and Perez-Hernandez, D. and Reimer, U. and Mertins, P. and Dittmar, G. and Leutz, A.
bioRxiv
: 2020.12.28.424569.
28 December 2020
Fructose 1,6-bisphosphate sensing by pyruvate kinase isozymes M2 (PKM2) controls MyoD stability and myogenic differentiation.
Kim, M. and Zhang, Y. and Birchmeier, C.
bioRxiv
: 2020.12.22.424062.
22 December 2020
Longitudinal omics in Syrian hamsters integrated with human data unravel complexity of moderate immune responses to SARS-CoV-2.
Nouailles, G. and Wyler, E. and Pennitz, P. and Postmus, D. and Vladimirova, D. and Kazmierski, J. and Pott, F. and Dietert, K. and Mülleder, M. and Farztdinov, V. and Obermayer, B. and Wienhold, S.M. and Andreotti, S. and Höfler, T. and Sawitzki, B. and Drosten, C. and Sander, L.E. and Suttorp, N. and Ralser, M. and Beule, D. and Gruber, A.D. and Goffinet, C. and Landthaler, M. and Trimpert, J. and Witzenrath, M.
bioRxiv
: 2020.12.18.423524.
19 December 2020
Local microcircuitry of parasubiculum shows distinct and common features of excitatory and inhibitory connectivity.
Sammons, R.P. and Tzilivaki, A. and Schmitz, D.
bioRxiv
: 2020.12.18.423400.
19 December 2020
GUNC: detection of chimerism and contamination in prokaryotic genomes.
Orakov, A. and Fullam, A. and Coelho, L.P. and Khedkar, S. and Szklarczyk, D. and Mende, D.R. and Schmidt, T.S.B. and Bork, P.
bioRxiv
: 2020.12.16.422776.
16 December 2020
IFT88 transports Gucy2d, a guanylyl cyclase, to maintain sensory cilia function in Drosophila.
Werner, S. and Zitouni, S. and Okenve-Ramos, P. and Mendonça, S. and Sporbert, A. and Spalthoff, C. and Göpfert, M.C. and Jana, S.C. and Bettencourt-Dias, M.
bioRxiv
: 2020.12.15.417840.
15 December 2020
Single-cell RNA sequencing reveals distinct tumor microenvironmental patterns in lung adenocarcinoma.
Bischoff, P. and Trinks, A. and Obermayer, B. and Pett, J.P. and Lehmann, A. and Jurmeister, P. and Elsner, A. and Dziodzio, T. and Rückert, J.C. and Neudecker, J. and Falk, C. and Beule, D. and Sers, C. and Morkel, M. and Horst, D. and Blüthgen, N. and Klauschen, F.
bioRxiv
: 2020.12.11.419606.
11 December 2020
Reconstitution of β-adrenergic regulation of Ca(V)1.2: Rad-dependent and Rad-independent protein kinase A mechanisms.
Katz, M. and Subramaniam, S. and Chomsky-Hecht, O. and Tsemakhovich, V. and Belkacemi, A. and Flockerzi, V. and Klussmann, E. and Hirsch, J. and Weiss, S. and Dascal, N.
bioRxiv
: 2020.11.30.403964.
1 December 2020
3D super-resolution fluorescence microscopy maps the variable molecular architecture of the nuclear pore complex.
Sabinina, V.J. and Hossain, M.J. and Hériché, J.K. and Hoess, P. and Nijmeijer, B. and Mosalaganti, S. and Kueblbeck, M. and Callegari, A. and Szymborska, A. and Beck, M. and Ries, J. and Ellenberg, J.
bioRxiv
: 2020.11.27.386599.
27 November 2020
The BTB transcription factors ZBTB11 and ZFP131 maintain pluripotency by pausing POL II at pro-differentiation genes.
Garipler, G. and Lu, C. and Morrissey, A. and Lopez-Zepeda, L.S. and Vidal, S.E. and Aydin, B. and Stadtfeld, M. and Ohler, U. and Mahony, S. and Sanjana, N.E. and Mazzoni, E.O.
bioRxiv
: 2020.11.23.391771.
23 November 2020
Spatio-temporal mRNA dynamics in the early zebrafish embryo.
Holler, K. and Neuschulz, A. and Drewe-Boß, P. and Mintcheva, J. and Spanjaard, B. and Arsiè, R. and Ohler, U. and Landthaler, M. and Junker, J.P.
bioRxiv
: 020.11.19.389809.
20 November 2020
MLL1 is required for maintenance of intestinal stem cells and the expression of the cell adhesion molecule JAML.
Goveas, N. and Waskow, C. and Arndt, K. and Heuberger, J. and Zhang, Q. and Alexopoulou, D. and Dahl, A. and Birchmeier, W. and Anastassiadis, K. and Stewart, A.F. and Kranz, A.
bioRxiv
: 2020.11.19.389528.
19 November 2020
SEMITONES: Single-cEll Marker IdentificaTiON by Enrichment Scoring.
Vlot, A.H.C. and Maghsudi, S. and Ohler, U.
bioRxiv
: 2020.11.17.386664.
18 November 2020
LoopDetect: comprehensive feedback loop detection in ordinary differential equation models.
Baum, K. and Wolf, J.
bioRxiv
: 2020.11.15.383703.
17 November 2020
Single-nuclei RNA-sequencing of plants.
Sunaga-Franze, D.Y. and Muino, J.M. and Braeuning, C. and Xu, X. and Zong, M. and Smaczniak, C. and Yan, W. and Fischer, C. and Vidal, R. and Kliem, M. and Kaufmann, K. and Sauer, S.
bioRxiv
: 2020.11.14.382812.
16 November 2020
The mechanotransduction protein STOML3 is required for functional plasticity following peripheral nerve regeneration.
Haseleu, J. and Walcher, J. and Lewin, G.R.
bioRxiv
: 2020.11.10.367748.
10 November 2020
Diverse chemotypes drive biased signaling by cannabinoid receptors.
Miljuš, T. and Heydenreich, F.M. and Gazzi, T. and Kimbara, A. and Rogers-Evans, M. and Nettekoven, M. and Zirwes, E. and Osterwald, A. and Rufer, A.C. and Ullmer, C. and Guba, W. and Le Gouill, C. and Fingerle, J. and Nazaré, M. and Grether, U. and Bouvier, M. and Veprintsev, D.B.
bioRxiv
: 2020.11.09.375162.
10 November 2020
Importin α7 deficiency causes infertility in male mice by disrupting spermatogenesis.
Liu, N. and Qadri, F. and Busch, H. and Huegel, S. and Sihn, G. and Chuykin, I. and Hartmann, E. and Bader, M. and Rother, F.
bioRxiv
: 2020.11.09.374652.
9 November 2020
Vascular cognitive impairment in the mouse reshapes visual, spatial network functional connectivity.
Hall, G.R. and Boehm-Sturm, P. and Dirnagl, U. and Finke, C. and Foddis, M. and Harms, C. and Koch, S.P. and Kuchling, J. and Madan, C.R. and Mueller, S. and Sassi, C. and Sotiropoulos, S.N. and Trueman, R.C. and Wallis, M. and Yildirim, F. and Farr, T.D.
bioRxiv
: 2020.11.04.366294.
5 November 2020
Identification of novel disease relevant genetic modifiers affecting the SHH pathway in the developing brain.
Mecklenburg, N. and Kowalczyk, I. and Witte, F. and Görne, J. and Laier, A. and Gonschior, H. and Lehmann, M. and Richter, M. and Sporbert, A. and Purfürst, B. and Hübner, N. and Hammes, A.
bioRxiv
: 2020.11.03.366302.
3 November 2020
Dual-view light-sheet imaging through tilted glass interface using a deformable mirror.
Vladimirov, N. and Preusser, F. and Wisniewski, J. and Yaniv, Z. and Desai, R.A. and Woehler, A. and Preibisch, S.
bioRxiv
: 2020.10.20.345306.
21 October 2020
SPLICE-q: a Python tool for genome-wide quantification of splicing efficiency.
Costa, V.R.M. and Pfeuffer, J. and Louloupi, A. and Ørom, U.A.V. and Piro, R.M.
bioRxiv
: 2020.10.12.318808.
12 October 2020
Olig3 acts as a master regulator of cerebellar development.
Lowenstein, E.D. and Rusanova, A. and Stelzer, J. and Hernaiz-Llorens, M. and Schroer, A.E. and Epifanova, E. and Bladt, F. and Isik, E.G. and Jia, S. and Tarabykin, V. and Hernandez-Miranda, L.R.
bioRxiv
: 2020.10.10.334615.
10 October 2020
Cargo-specific recruitment in clathrin and dynamin-independent endocytosis.
Moreno-Layseca, P. and Jäntti, N.Z. and Godbole, R. and Sommer, C. and Jacquemet, G. and Al-Akhrass, H. and Kronqvist, P. and Kallionpää, R.E. and Oliveira-Ferrer, L. and Cervero, P. and Linder, S. and Aepfelbacher, M. and Rae, J. and Parton, R.G. and Disanza, A. and Scita, G. and Mayor, S. and Selbach, M. and Veltel, S. and Ivaska, J.
bioRxiv
: 2020.10.05.323295.
5 October 2020
Morphine alleviates pain after heart cryoinjury in zebrafish without impeding regeneration.
Lelek, S. and Simões, M. and Hu, B. and Alameldeen, A.M.A. and Czajkowski, M.T. and Meyer, A.M. and Ferrara, F. and Junker, J.P. and Panáková, D.
bioRxiv
: 2020.10.01.322560.
2 October 2020
The zinc finger antiviral protein ZAP destabilises viral transcripts and restricts human cytomegalovirus.
Gonzalez-Perez, A.C. and Stempel, M. and Wyler, E. and Urban, C. and Piras, A. and Hennig, T. and Heim, A. and Landthaler, M. and Pichlmair, A. and Erhard, F. and Dölken, L. and Brinkmann, M.M.
bioRxiv
: 2020.09.15.297804.
17 September 2020
Targeted proteomics reveals quantitative differences in low abundance glycosyltransferases of patients with congenital disorders of glycosylation.
Sakson, R. and Beedgen, L. and Bernhard, P. and Alp, K.M. and Lübbehusen, N. and Röth, R. and Niesler, B. and Mayer, M.P. and Thiel, C. and Ruppert, T.
bioRxiv
: 2020.09.15.291732.
16 September 2020
Wasp controls oriented migration of endothelial cells to achieve functional vascular patterning.
Rosa, A. and Giese, W. and Meier, K. and Alt, S. and Klaus-Bergmann, A. and Edgar, L.T. and Bartels, E. and Collins, R. and Szymborska-Mell, A. and Coxam, B. and Bernabeu, M.O. and Gerhardt, H.
bioRxiv
: 2020.09.15.296574.
15 September 2020
RBM20 phosphorylation on serine/arginine domain is crucial to regulate pre-mRNA splicing and protein shuttling in the heart.
Sun, M. and Jin, Y. and Zhu, C. and Zhang, Y. and Liss, M. and Gotthardt, M. and Ren, J. and Ge, Y. and Guo, W.
bioRxiv
: 2020.09.15.297002.
15 September 2020
Myogenic vasoconstriction requires canonical Gq/11 signaling of the angiotensin II type 1a receptor in the murine vasculature.
Cui, Y. and Kassmann, M. and Nickel, S. and Zhang, C. and Alenina, N. and Anistan, Y.M. and Schleifenbaum, J. and Bader, M. and Welsh, D.G. and Huang, Y. and Gollasch, M.
bioRxiv
: 2020.09.09.289280.
11 September 2020
Mechanistic basis for motor-driven membrane constriction by dynamin.
Ganichkin, O. and Vancraenenbroeck, R. and Rosenblum, G. and Hofmann, H. and Mikhailov, A.S. and Daumke, O. and Noel, J.K.
bioRxiv
: 2020.09.10.289546.
11 September 2020
FRC-QE: a robust and comparable 3D microscopy image quality metric for cleared organoids.
Preusser, F. and dos Santos, N. and Contzen, J. and Stachelscheid, H. and Costa, E.T. and Mergenthaler, P. and Preibisch, S.
bioRxiv
: 2020.09.10.291286.
11 September 2020
The CONDOR pipeline for simultaneous knockdown of multiple genes identifies RBBP-5 as a germ cell reprogramming barrier in C. elegans.
Kazmierczak, M. and Díaz, C.F. and Ofenbauer, A. and Tursun, B.
bioRxiv
: 2020.09.01.276972.
1 September 2020
Increased and synchronous recruitment of release sites underlies hippocampal mossy fiber presynaptic potentiation.
Orlando, M. and Dvorzhak, A. and Bruentgens, F. and Maglione, M. and Rost, B.R. and Sigrist, S.J. and Breustedt, Jm and Schmitz, D.
bioRxiv
: 2020.08.21.260638.
21 August 2020
A SARS-CoV-2 neutralizing antibody protects from lung pathology in a COVID-19 hamster model.
Kreye, J. and Reincke, S.M. and Kornau, H.C. and Sanchez-Sendin, E. and Corman, V.M. and Liu, H. and Yuan, M. and Wu, N.C. and Zhu, X. and Lee, C.C.D. and Trimpert, J. and Hoeltje, M. and Dietert, K. and Stoeffler, L. and von Wardenburg, N. and van Hoof, S. and Homeyer, M.A. and Hoffmann, J. and Abdelgawad, A. and Gruber, A.D. and Bertzbach, L.D. and Vladimirova, D. and Li, L.Y. and Barthel, P.C. and Skriner, K. and Hocke, A.C. and Hippenstiel, S. and Witzenrath, M. and Suttorp, N. and Kurth, F. and Franke, C. and Endres, M. and Schmitz, D. and Jeworowski, L.M. and Richter, A. and Schmidt, M.L. and Schwarz, T. and Mueller, M.A. and Drosten, C. and Wendisch, D. and Sander, L.E. and Osterrieder, N. and Wilson, I.A. and Pruess, H.
bioRxiv
: 2020.08.15.252320.
16 August 2020
Assessment of ethanol-induced toxicity on iPSC-derived human dopaminergic neurons using a novel high-throughput mitochondrial neuronal health (MNH) assay.
Zink, A. and Conrad, J. and Telugu, N.S. and Diecke, S. and Heinz, A. and Wanker, E.E. and Priller, J. and Prigione, A.
bioRxiv
: 2020.08.12.237461.
12 August 2020
CD40 provides immune privilege to the bone marrow hematopoietic niche.
Bassani, B. and Gulino, A. and Portararo, P. and Botti, L. and Cappetti, B. and Chiodoni, C. and Bolli, N. and Ciciarello, M. and Joehrens, K. and Anagnostopoulos, I. and Na, I.K. and Curti, A. and Tripodo, C. and Colombo, M.P. and Sangaletti, S.
bioRxiv
: 2020.08.10.243691.
10 August 2020
Deep learning assisted peak curation for large scale LC-MS Metabolomics.
Gloaguen, Y. and Kirwan, J. and Beule, D.
bioRxiv
: 2020.08.09.242727.
10 August 2020
Quantitative lineage analysis identifies a long-term progenitor niche for the hepato-pancreato-biliary organ system.
Willnow, D. and Benary, U. and Margineanu, A. and Vignola, M.L. and Pongrac, I.M. and Karimaddini, Z. and Vigilante, A. and Wolf, J. and Spagnoli, F.M.
bioRxiv
: 2020.08.06.240176.
6 August 2020
Multiplex-GAM: genome-wide identification of chromatin contacts yields insights not captured by Hi-C.
Beagrie, R.A. and Thieme, C.J. and Annunziatella, C. and Baugher, C. and Zhang, Y. and Schueler, M. and Kramer, D.C.A. and Chiariello, A.M. and Bianco, S. and Kukalev, A. and Li, Y. and Kempfer, R. and Scialdone, A. and Welch, L.R. and Nicodemi, M. and Pombo, A.
bioRxiv
: 2020.07.31.230284.
31 July 2020
Parallel genetics of regulatory sequences in vivo.
Froehlich, J. and Uyar, B. and Herzog, M. and Theil, K. and Glažar, P. and Akalin, A. and Rajewsky, N.
bioRxiv
: 2020.07.28.224998.
29 July 2020
Megadalton-sized dityrosine aggregates of α-synuclein retain high degrees of structural disorder and internal dynamics.
Verzini, S. and Shah, M. and Theillet, F.X. and Belsom, A. and Bieschke, J. and Wanker, E.E. and Rappsilber, J. and Binolfi, A. and Selenko, P.
bioRxiv
: 2020.07.26.202358.
26 July 2020
A semi-automated intestinal organoid screening method demonstrates epigenetic control of epithelial maturation.
Ostrop, J. and Zwiggelaar, R. and Pedersen, M.T. and Gerbe, F. and Bösl, K. and Lindholm, H.T. and Díez-Sánchez, Al. and Parmar, N. and Radetzki, S. and von Kries, J.P. and Jay, P. and Jensen, K.B. and Arrowsmith, C. and Oudhoff, M.J.
bioRxiv
: 2020.07.23.217414.
24 July 2020
Variability of an early developmental cell population underlies stochastic laterality defects.
Moreno-Ayala, R. and Olivares-Chauvet, P. and Schäfer, R. and Junker, J.P.
bioRxiv
: 2020.07.20.212282.
20 July 2020
Open Source ImmGen: network perspective on metabolic diversity among mononuclear phagocytes.
Gainullina, A. and Huang, L.H. and Todorov, H. and Kim, K. and Yng, L.S. and Kent, A. and Jia, B. and Seddu, K. and Krchma, K. and Wu, J. and Crozat, K. and Tomasello, E. and Narang, V. and Dress, R. and See, P. and Scott, C. and Gibbings, S. and Bajpai, G. and Desai, J.V. and Maier, B. and This, S. and Wang, P. and Aguilar, S.V. and Poupel, L. and Dussaud, S. and Zhou, T.A. and Angeli, V. and Blander, J.M. and Choi, K. and Dalod, M. and Dzhagalov, I. and Gautier, E.L. and Jakubzick, C. and Lavine, K. and Lionakis, M.S. and Paidassi, H. and Sieweke, M.H. and Ginhoux, Fl. and Guilliams, M. and Benoist, C. and Merad, M. and Randolph, G.J. and Sergushichev, A. and Artyomov, M.N.
bioRxiv
: 2020.07.15.204388.
16 July 2020
Neural tube closure requires the endocytic receptor Lrp2 and its functional interaction with intracellular scaffolds.
Kowalczyk, I. and Lee, C. and Schuster, E. and Hoeren, J. and Trivigno, V. and Riedel, L. and Goerne, J. and Wallingford, J.B. and Hammes-Lewin, A. and Feistel, K.
bioRxiv
: 2020.07.15.205252.
16 July 2020
Pairwise interactions in adjuvant combinations dictate immune responses and inform cancer immunotherapy design.
Pandey, S. and Gruenbaum, A. and Kanashova, T. and Mertins, P. and Cluzel, P. and Chevrier, N.
bioRxiv
: 2020.07.11.198879.
12 July 2020
CTCF mediates dosage and sequence-context-dependent transcriptional insulation through formation of local chromatin domains.
Huang, H. and Zhu, Q. and Jussila, A. and Han, Y. and Bintu, B. and Kern, C. and Conte, M. and Zhang, Y. and Bianco, S. and Chiariello, A.M. and Yu, M. and Hu, R. and Juric, I. and Hu, M. and Nicodemi, M. and Zhuang, X. and Ren, B.
bioRxiv
: 2020.07.07.192526.
8 July 2020
Neuronal autophagy regulates presynaptic neurotransmission by controlling the axonal endoplasmic reticulum.
Kuijpers, M. and Kochlamazashvili, G. and Stumpf, A. and Puchkov, D. and Lucht, M.T. and Krause, E. and Schmitz, D. and Haucke, V.
bioRxiv
: 2020.07.06.189522.
6 July 2020
Targeting the ubiquitin-proteasome system in a pancreatic cancer subtype with hyperactive MYC.
Lankes, K. and Hassan, Z. and Doffo, M.J. and Schneeweis, C. and Lier, S. and Öllinger, R. and Rad, R. and Krämer, O.H. and Keller, U. and Saur, D. and Reichert, M. and Schneider, G. and Wirth, M.
bioRxiv
: 2020.07.01.182162.
2 July 2020
USH2A is a skin end-organ protein necessary for vibration sensing in mice and humans.
Schwaller, F. and Bégay, V. and García-García, G. and Taberner, F.J. and Moshourab, R. and McDonald, B. and Docter, T. and Kühnemund, J. and Ojeda-Alonso, J. and Paricio-Montesinos, R. and Lechner, S.G. and Poulet, J.F.A. and Millan, J.M. and Lewin, G.R.
bioRxiv
: 2020.07.01.180919.
2 July 2020
Structural and functional characterization of allatostatin receptor type-C of Thaumetopoea pityocampa revealed the importance of Q271(6.55) residue in G protein-dependent activation pathway.
Shahraki, A. and Isbilir, A. and Dogan, B. and Lohse, M.J. and Durdagi, S. and Birgul-Iyison, N.
bioRxiv
: 2020.07.01.174037.
2 July 2020
A single cell Arabidopsis root atlas reveals developmental trajectories in wild type and cell identity mutants.
Shahan, R. and Hsu, C.W. and Nolan, T.M. and Cole, B.J. and Taylor, I.W. and Vlot, A.H.C. and Benfey, P.N. and Ohler, U.
bioRxiv
: 2020.06.29.178863.
30 June 2020
Regional expression profiles of risk genes for depression are associated with brain activation patterns in emotion and reward tasks.
Komorowski, A. and Vidal, R. and Singh, A. and Murgaš, M. and Pena-Centeno, T. and Gryglewski, G. and Kasper, S. and Wiltfang, J. and Lanzenberger, R. and Goya-Maldonado, R.
bioRxiv
: 2020.06.27.175257.
27 June 2020
Single-cell-resolved dynamics of chromatin architecture delineate cell and regulatory states in wildtype and cloche/npas4l mutant zebrafish embryos.
McGarvey, A.C. and Kopp, W. and Vučićević, D. and Kempfer, R. and Mattonet, K. and Hirsekorn, A. and Bilić, I. and Trinks, A. and Merks, A.M. and Panáková, D. and Pombo, A. and Akalin, A. and Junker, J.P. and Stainier, D.Y.R. and Garfield, D. and Ohler, U. and Lacadie, S.A.
bioRxiv
: 2020.06.26.173377.
26 June 2020
Integrative analysis of genomic variants reveals new associations of candidate haploinsufficient genes with congenital heart disease.
Audain, E. and Wilsdon, A. and Breckpot, J. and Izarzugaza, J.M.G. and Fitzgerald, T.W. and Kahlert, A.K. and Sifrim, A. and Wünnemann, F. and Perez-Riverol, Y. and Abdul-Khaliq, H. and Bak, M. and Bassett, A.S. and Belmont, J.W. and Benson, D.W. and Berger, F. and Daehnert, I. and Devriendt, K. and Dittrich, S. and Daubeney, P. and Garg, V. and Hackmann, K. and Hoff, K. and Hofmann, P. and Dombrowsky, G. and Pickardt, T. and Bauer, U. and Keavney, B.D. and Klaassen, S. and Kramer, H.H. and Marshall, C.R. and Milewicz, D.M. and Lemaire, S.A. and Coselli, J. and Mitchell, M.E. and Tomita-Mitchell, A. and Prakash, S.K. and Stamm, K. and Stewart, A.F.R. and Silversides, C.K. and Siebert, R. and Stiller, B. and Rosenfeld, J.A. and Vater, I. and Postma, A.V. and Caliebe, A. and Brook, J.D. and Andelfinger, G. and Hurles, M.E. and Thienpont, B. and Larsen, L.A. and Hitz, M.P.
bioRxiv
: 2020.06.25.169573.
25 June 2020
Deciphering the regulatory logic of a Drosophila enhancer through systematic sequence mutagenesis and quantitative image analysis.
Le Poul, Y. and Xin, Y. and Ling, L. and Mühling, B. and Jaenichen, R. and Hörl, D. and Bunk, D. and Harz, H. and Leonhardt, H. and Wang, Y. and Osipova, E. and Museridze, M. and Dharmadhikari, D. and Murphy, E. and Rohs, R. and Preibisch, S. and Prud'homme, B. and Gompel, N.
bioRxiv
: 2020.06.24.169748.
25 June 2020
Rub1/NEDD8, a ubiquitin-like modifier, is also a ubiquitin modifier.
Zerath Gurevich, S. and Sinha, A. and Longworth, J. and Singh, R.K. and Lemma, B.E. and Thakur, A. and Popp, O. and Kornitzer, D. and Reis, N. and Scheffner, M. and Dittmar, G. and Pick, E. and Fushman, D. and Glickman, M.H.
bioRxiv
: 2020.06.18.159145.
19 June 2020
HNRNPM controls circRNA biogenesis and splicing fidelity to sustain prostate cancer cell fitness.
Ho, J.S.Y. and Low, D. and Schwarz, M. and Incarnato, D. and Gay, F. and Tabaglio, T. and Zhang, J. and Wollman, H. and Chen, L. and An, O. and Chan, T.H.M. and Hickman, A.H. and Zheng, S. and Roudko, V. and Chen, S. and Ahmed, M. and He, H.H. and Greenbaum, B.D. and Marazzi, I. and Serresi, M. and Gargiulo, G. and Oliviero, S. and Wee, D.K.B. and Guccione, E.
bioRxiv
: 2020.06.17.157537.
18 June 2020
HMGXB4 targets Sleeping Beauty transposition to vertebrate germinal stem sells.
Devaraj, A. and Singh, M. and Narayanavari, S. and Yong, G. and Wang, J. and Wang, J. and Becker, M. and Walisko, O. and Schorn, A. and Cseresznyés, Z. and Grzela, D. and Raskó, T. and Selbach, M. and Ivics, Z. and Izsvák, Z.
bioRxiv
: 2020.06.15.145656.
15 June 2020
State-dependent signatures of anti-NMDA-receptor encephalitis: a dynamic functional connectivity study.
von Schwanenflug, N. and Krohn, S. and Heine, J. and Paul, F. and Pruess, H. and Finke, C.
bioRxiv
: bioRxiv:2020.06.12.141945.
12 June 2020
YAP and β-catenin co-operate to drive oncogenesis in basal breast cancer.
Quinn, H. and Koren, E. and Vogel, R. and Popp, O. and Mertins, P. and Messerschmidt, C. and Marangoni, E. and Fuchs, Y. and Birchmeier, W.
bioRxiv
: 2020.06.05.115881.
6 June 2020
Trans control of cardiac mRNA translation in a protein length-dependent fashion.
Witte, F. and Ruiz-Orera, J. and Ciolli Mattioli, C. and Blachut, S. and Adami, E. and Schulz, J.F. and Schneider-Lunitz, V. and Hummel, O. and Patone, G. and Mücke, M.B. and Šilhavý, J. and Heinig, M. and Bottolo, L. and Sanchis, D. and Vingron, M. and Chekulaeva, M. and Pravenec, M. and Hubner, N. and van Heesch, S.
bioRxiv
: 020.06.05.133298.
6 June 2020
Human endogenous retrovirus K Rec forms a regulatory loop with MITF that opposes the progression of melanoma to an invasive stage.
Singh, M. and Cai, H. and Bunse, M. and Feschotte, C. and Izsvak, Z.
bioRxiv
: 2020.05.27.120170.
2 June 2020
Serotonin suppresses slow oscillations by activating somatostatin interneurons via the 5-HT(2A) receptor.
de Filippo, R. and Rost, B. and Stumpf, A. and Cooper, C. and Tukker, J.J. and Harms, C. and Beed, P. and Schmitz, D.
bioRxiv
: 2020.05.26.113373.
26 May 2020
Association between erythrocyte dynamics and vessel remodelling in developmental vascular networks.
Zhou, Q. and Perovic, T. and Fechner, I. and Edgar, L.T. and Hoskins, P.R. and Gerhardt, H. and Krüger, T. and Bernabeu, M.O.
bioRxiv
: 2020.05.21.106914.
23 May 2020
Dissecting HSV-1-induced host shut-off at RNA level.
Friedel, C.C. and Whisnant, A.W. and Djakovic, L. and Rutkowski, A.J. and Friedl, M.S. and Kluge, M. and Williamson, J.C. and Sai, S. and Oliveira Vidal, R. and Sauer, S. and Hennig, T. and Prusty, B. and Lehner, P.J. and Matheson, N.J. and Erhard, F. and Dölken, L.
bioRxiv
: 2020.05.20.106039.
20 May 2020
Host genetic and environmental factors shape the human gut resistome.
Le Roy, C.I. and Bowyer, R.C.E. and Carr, V.R. and Costeira, R. and Castillo-Fernandez, J.E.R. and Martin, T.C. and Spector, T. and Steves, C. and Moyes, D. and Forslund, S.K. and Bell, J.T.
bioRxiv
: 2020.05.18.092973.
20 May 2020
Enzymatic dissociation induces transcriptional and proteotype bias in brain cell populations.
Mattei, D. and Ivanov, A. and van Oostrum, M. and Pantelyushin, S. and Richetto, J. and Mueller, F. and Beffinger, M. M. and Schellhammer, L. and vom Berg, J. and Wollscheid, B. and Beule, D. and Paolicelli, R.C. and Meyer, U.
bioRxiv
: 2020.05.14.095422.
16 May 2020
A homology independent sequence replacement strategy in human cells using a CRISPR nuclease.
Danner, E.W. and Lebedin, M. and de la Rosa, K. and Kühn, R.
bioRxiv
: 2020.05.11.088252.
12 May 2020
Single cell RNA-sequencing-based analysis of CD4(+) T-cell subset-specific susceptibility to transcriptional modulation by HIV-1 latency-reversing agents.
Kazmierski, J. and Postmus, D. and Wyler, E. and Fischer, C. and Jansen, J. and Meixenberger, K. and Vitcetz, S.N. and Sohn, M. and Sauer, S. and Bannert, N. and Landthaler, M. and Goffinet, C.
bioRxiv
: 2020.05.04.075119.
5 May 2020
Bulk and single-cell gene expression profiling of SARS-CoV-2 infected human cell lines identifies molecular targets for therapeutic intervention.
Wyler, E. and Mösbauer, K. and Franke, V. and Diag, A. and Gottula, L.T. and Arsie, R. and Klironomos, F. and Koppstein, D. and Ayoub, S. and Buccitelli, C. and Richter, A. and Legnini, I. and Ivanov, A. and Mari, T. and Del Giudice, S. and Papies, J.P. and Müller, M.A. and Niemeyer, D. and Selbach, M. and Akalin, A. and Rajewsky, N. and Drosten, C. and Landthaler, M.
bioRxiv
: 2020.05.05.079194.
5 May 2020
Cdon mutation and fetal alcohol converge on nodal signaling in a gene-environment interaction model of holoprosencephaly.
Hong, M. and Christ, A. and Christa, A. and Willnow, T.E. and Krauss, R.S.
bioRxiv
: 2020.04.30.070870.
1 May 2020
A functional screen of translated pancreatic lncRNAs identifies a microprotein-independent role for LINC00261 in endocrine cell differentiation.
Gaertner, B. and van Heesch, S. and Schneider-Lunitz, V. and Schulz, J.F. and Witte, F. and Blachut, S. and Nguyen, S. and Wong, R. and Matta, I. and Hubner, N. and Sander, M.
bioRxiv
: 2020.04.28.062679.
29 April 2020
Comparison of the Hi-C, GAM and SPRITE methods by use of polymer models of chromatin.
Fiorillo, L. and Musella, F. and Kempfer, R. and Chiariello, A.M. and Bianco, S. and Kukalev, A. and Irastorza-Azcarate, I. and Esposito, A. and Conte, M. and Prisco, A. and Pombo, A. and Nicodemi, M.
bioRxiv
: 2020.04.24.059915.
25 April 2020
Vasohibin-1 mediated tubulin detyrosination selectively regulates secondary sprouting and lymphangiogenesis in the zebrafish trunk.
Bastos de Oliveira, M. and Meier, K. and Coxam, B. and Geudens, I. and Jung, S. and Szymborska, A. and Gerhardt, H.
bioRxiv
: 2020.04.23.053256.
23 April 2020
Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells.
Muus, C. and Luecken, M.D. and Eraslan, G. and Waghray, A. and Heimberg, G. and Sikkema, L. and Kobayashi, Y. and Vaishnav, E.D. and Subramanian, A. and Smilie, C. and Jagadeesh, K. and Thu Duong, E. and Fiskin, E. and Torlai Triglia, E. and Ansari, M. and Cai, P. and Lin, B. and Buchanan, J. and Chen, S. and Shu, J. and Haber, A.L. and Chung, H. and Montoro, D.T. and Adams, T. and Aliee, H. and Allon, S.J. and Andrusivova, A.Z. and Angelidis, I. and Ashenberg, O. and Bassler, K. and Bécavin, C. and Benhar, I. and Bergenstråhle, J. and Bergenstråhle, L. and Bolt, L. and Braun, E. and Bui, L.T. and Chaffin, M. and Chichelnitskiy, E. and Chiou, J. and Conlon, T.M. and Cuoco, M.S. and Deprez, M. and Fischer, D.S. and Gillich, A. and Gould, J. and Guo, M. and Gutierrez, A.J. and Habermann, A.C. and Harvey, T. and He, P. and Hou, X. and Hu, L. and Jaiswal, A. and Jiang, P. and Kapellos, T. and Kuo, C.S. and Larsson, L. and Leney-Greene, M.A. and Lim, K. and Litviňuková, M. and Lu, J. and Ludwig, L.S. and Luo, W. and Maatz, H. and Madissoon, E. and Mamanova, L. and Manakongtreecheep, K. and Marquette, C.H. and Mbano, I. and McAdams, A.M. and Metzger, R.J. and Nabhan, A.N. and Nyquist, S.K. and Penland, L. and Poirion, O.B. and Poli, S. and Qi, C.C. and Queen, R. and Reichart, D. and Rosas, I. and Schupp, J. and Sinha, R. and Sit, R.V. and Slowikowski, K. and Slyper, M. and Smith, N. and Sountoulidis, A. and Strunz, M. and Sun, D. and Talavera-López, C. and Tan, P. and Tantivit, J. and Travaglini, K.J. and Tucker, N.R. and Vernon, K. and Wadsworth, M.H. and Waldman, J. and Wang, X. and Yan, W. and Zhao, W. and Ziegler, C.G.K.
bioRxiv
: 2020.04.19.049254.
21 April 2020
A CRISPR-Cas9-engineered mouse model for GPI anchor deficiency mirrors human phenotype and shows hippocampal synaptic dysfunctions.
Rodríguez de los Santos, M. and Rivalan, M. and David, F.S. and Knaus, A. and Stumpf, A. and Velasquez, L.M. and Voigt, A. and Mattei, D. and Long, M. and Vogt, G. and Wittler, L. and Timmermann, B. and Robinson, P.N. and Horn, D. and Mundlos, S. and Kornak, U. and Schmitz, D. and Winter, Y. and Krawitz, P.M.
bioRxiv
: 2020.04.20.050591.
21 April 2020
Single-nucleus transcriptomics reveals functional compartmentalization in syncytial skeletal muscle cells.
Kim, M. and Franke, V. and Brandt, B. and Spuler, S. and Akalin, A. and Birchmeier, C.
bioRxiv
: 2020.04.14.041665.
15 April 2020
Co-activation of NF-κB and MYC renders cancer cells addicted to IL6 for survival and phenotypic stability.
Barbosa, R.R. and Xu, A.Q. and D'Andrea, D. and Copley, F. and Patel, H. and Chakravarty, P. and Clear, A. and Calaminici, M. and Janz, M. and Zhang, B. and Schmidt-Supprian, M. and Wang, J. and Gribben, J.G. and Tooze, R. and Fitzgibbon, J. and Franzoso, G. and Rajewsky, K. and Calado, D.P.
bioRxiv
: 2020.04.12.038414.
13 April 2020
Mapping the unique and shared functions of oncogenic KRAS and RIT1 with proteome and transcriptome profiling.
Lo, A. and Holmes, K. and Mundt, F. and Moorthi, S. and Fung, I. and Fereshetian, S. and Watson, J. and Carr, S.A. and Mertins, P. and Berger, A.H.
bioRxiv
: 2020.04.10.030460.
11 April 2020
Cells and gene expression programs in the adult human heart.
Litviňuková, M. and Talavera-López, C. and Maatz, H. and Reichart, D. and Worth, C.L. and Lindberg, E.L. and Kanda, M. and Polanski, K. and Fasouli, E.S. and Samari, S. and Roberts, K. and Tuck, L. and Heinig, M. and DeLaughter, D.M. and McDonough, B. and Wakimoto, H. and Gorham, J.M. and Nadelmann, E.R. and Mahbubani, K.T. and Saeb-Parsy, K. and Patone, G. and Boyle, J.J. and Zhang, H. and Zhang, H. and Viveiros, A. and Oudit, G.Y. and Bayraktar, O. and Seidman, J.G. and Seidman, C. and Noseda, M. and Hübner, N. and Teichmann, S.A.
bioRxiv
: 2020.04.03.024075.
10 April 2020
A connectome and analysis of the adult Drosophila central brain.
Scheffer, L.K. and Xu, C.S. and Januszewski, M. and Lu, Z. and Takemura, S. and Hayworth, K.J. and Huang, G.B. and Shinomiya, K. and Maitin-Shepard, J. and Berg, S. and Clements, J. and Hubbard, P. and Katz, W. and Umayam, L. and Zhao, T. and Ackerman, D. and Blakely, T. and Bogovic, J. and Dolafi, T. and Kainmueller, D. and Kawase, T. and Khairy, K.A. and Leavitt, L. and Li, P.H. and Lindsey, L. and Neubarth, N. and Olbris, D.J. and Otsuna, H. and Trautman, E.T. and Ito, M. and Goldammer, J. and Wolff, T. and Svirskas, R. and Schlegel, P. and Neace, E.R. and Knecht, C.J. and Alvarado, C.X. and Bailey, D.A. and Ballinger, S. and Borycz, J.A and Canino, B.S. and Cheatham, N. and Cook, M. and Dreher, M. and Duclos, O. and Eubanks, B. and Fairbanks, K. and Finley, S. and Forknall, N. and Francis, A. and Hopkins, G.P. and Joyce, E.M. and Kim, S.J. and Kirk, N.A. and Kovalyak, J. and Lauchie, S.A. and Lohff, A. and Maldonado, C. and Manley, E.A. and McLin, S. and Mooney, C. and Ndama, M. and Ogundeyi, O. and Okeoma, N. and Ordish, C. and Padilla, N. and Patrick, C. and Paterson, T. and Phillips, E.E. and Phillips, E.M. and Rampally, N. and Ribeiro, C. and Robertson, M.K. and Rymer, J.T. and Ryan, S.M. and Sammons, M. and Scott, A.K. and Scott, A.L. and Shinomiya, A. and Smith, C. and Smith, K. and Smith, N.L. and Sobeski, M.A. and Suleiman, A. and Swift, J. and Takemura, S. and Talebi, I. and Tarnogorska, D. and Tenshaw, E. and Tokhi, T. and Walsh, J.J. and Yang, T. and Horne, J.A. and Li, F. and Parekh, R. and Rivlin, P.K. and Jayaraman, V. and Ito, K. and Saalfeld, S. and George, R. and Meinertzhagen, I.A. and Rubin, G.M. and Hess, H.F. and Jain, V. and Plaza, S.M.
bioRxiv
: 2020.04.07.030213.
9 April 2020
SynaptoPAC, an optogenetic tool for induction of presynaptic plasticity.
Oldani, S. and Moreno-Velasquez, L. and Stumpf, A. and Rosenmund, C. and Schmitz, D. and Rost, B.R.
bioRxiv
: 2020.03.27.011635.
27 March 2020
Resolving fate and transcriptome of hematopoietic stem cell clones.
Pei, W. and Shang, F. and Wang, X. and Fanti, A.K. and Greco, A. and Busch, K. and Klapproth, K. and Zhang, Q. and Quedenau, C. and Sauer, S. and Feyerabend, T.B. and Höfer, T. and Rodewald, H.R.
bioRxiv
: 2020.03.25.008433.
26 March 2020
Single-cell analysis of the 3D topologies of genomic loci using genome architecture mapping.
Welch, L.R. and Baugher, C. and Zhang, Y. and Davis, T. and Marzluff, W.F. and Welch, J.D. and Pombo, A.
bioRxiv
: 2020.02.10.941047.
13 February 2020
PHF3 regulates neuronal gene expression through the new Pol II CTD reader domain SPOC.
Appel, L.M. and Franke, V. and Bruno, M. and Grishkovskaya, I. and Kasiliauskaite, A. and Schoeberl, U.E. and Puchinger, M.G. and Kostrhon, S. and Beltzung, E. and Mechtler, K. and Lin, G. and Vlasova, A. and Leeb, M. and Pavri, R. and Stark, A. and Akalin, A. and Stefl, R. and Bernecky, C. and Djinovic-Carugo, K. and Slade, D.
bioRxiv
: 2020.02.11.943159.
12 February 2020
CRNKL1 is a highly selective regulator of intron-retaining HIV-1 and cellular mRNAs.
Xiao, H. and Wyler, E. and Milek, M. and Grewe, B. and Kirchner, P. and Ekici, A. and Villela Silva, A.B.O. and Jungnickl, D. and Landthaler, M. and Ensser, A. and Überla, K.
bioRxiv
: 2020.02.04.934927.
11 February 2020
The architecture of protein synthesis in the developing neocortex at near-atomic resolution reveals Ebp1-mediated neuronal proteostasis at the 60S tunnel exit.
Kraushar, M.L. and Krupp, F. and Turko, P. and Ambrozkiewicz, M.C. and Sprink, T. and Imami, K. and Vieira-Vieira, C.H. and Schaub, T. and Harnett, D. and Münster-Wandowski, A. and Bürger, J. and Zinnall, U. and Borisova, E. and Yamamoto, H. and Rasin, M.R. and Beule, D. and Landthaler, M. and Mielke, T. and Tarabykin, V. and Vida, I. and Selbach, M. and Spahn, C.M.T.
bioRxiv
: 2020.02.08.939488.
10 February 2020
On the preservation of vessel bifurcations during flow-mediated angiogenic remodelling.
Edgar, L.T. and Franco, C.A. and Gerhardt, H. and Bernabeu, M.O.
bioRxiv
: 2020.02.07.938522.
7 February 2020
Pdap1 protects mature B lymphocytes from stress-induced cell death and promotes antibody gene diversification.
Delgado-Benito, V. and Berruezo-Llacuna, M. and Altwasser, R. and Winkler, W. and Balasubramanian, S. and Sundaravinayagam, D. and Graf, R. and Rahjouei, A. and Driesner, M. and Keller, L. and Janz, M. and Akalin, A. and Di Virgilio, M.
bioRxiv
: 2020.01.30.917062.
31 January 2020
VarFish - Collaborative and comprehensive variant analysis for diagnosis and research.
Holtgrewe, M. and Stolpe, O. and Nieminen, M. and Mundlos, S. and Knaus, A. and Kornak, U. and Seelow, D. and Segebrecht, L. and Spielmann, M. and Fischer-Zirnsak, B. and Boschann, F. and Scholl, U. and Ehmke, N. and Beule, D.
bioRxiv
: 2020.01.27.921965.
31 January 2020
GAMIBHEAR: whole-genome haplotype reconstruction from genome architecture mapping data.
Markowski, J. and Kempfer, R. and Kukalev, A. and Irastorza-Azcarate, I. and Loof, G. and Pombo, A. and Schwarz, R.F.
bioRxiv
: 2020.01.30.927061.
31 January 2020
USP15 deubiquitinase safeguards hematopoiesis and genome integrity in hematopoietic stem cells and leukemia cells.
van den Berk, P. and Lancini, C. and Company, C. and Serresi, M. and Hulsman, D. and Pritchard, C. and Song, J.Y. and Schmitt, M.J. and Tanger, E. and Huijbers, I.J. and Jacobs, H. and van Lohuizen, M. and Gargiulo, G. and Citterio, E.
bioRxiv
: 2020.01.23.916627.
24 January 2020
A connectome of the adult drosophila central brain.
Xu, C.S. and Januszewski, M. and Lu, Z. and Takemura, S. and Hayworth, K.J. and Huang, G. and Shinomiya, K. and Maitin-Shepard, J. and Ackerman, D. and Berg, S. and Blakely, T. and Bogovic, J. and Clements, J. and Dolafi, T. and Hubbard, P. and Kainmueller, D. and Katz, W. and Kawase, T. and Khairy, K.A. and Leavitt, L. and Li, P.H. and Lindsey, L. and Neubarth, N. and Olbris, D.J. and Otsuna, H. and Troutman, E.T. and Umayam, L. and Zhao, T. and Ito, M. and Goldammer, J. and Wolff, T. and Svirskas, R. and Schlegel, P. and Neace, E.R. and Knecht, C.J. and Alvarado, C.X. and Bailey, D.A. and Ballinger, S. and Borycz, J.A. and Canino, B.S. and Cheatham, N. and Cook, M. and Dreher, M. and Duclos, O. and Eubanks, B. and Fairbanks, K. and Finley, S. and Forknall, N. and Francis, A. and Hopkins, G.P. and Joyce, E.M. and Kim, S.J. and Kirk, N.A. and Kovalyak, J. and Lauchie, S.A. and Lohff, A. and Maldonado, C. and Manley, E.A. and McLin, S. and Mooney, C. and Ndama, M. and Ogundeyi, O. and Okeoma, N. and Ordish, C. and Padilla, N. and Patrick, C. and Paterson, T. and Phillips, E.E. and Phillips, E.M. and Rampally, N. and Ribeiro, C. and Robertson, M.K. and Rymer, J.T. and Ryan, S.M. and Sammons, M. and Scott, A.K. and Scott, A.L. and Shinomiya, A. and Smith, C. and Smith, K. and Smith, N.L. and Sobeski, M.A. and Suleiman, A. and Swift, J. and Takemura, S. and Talebi, I. and Tarnogorska, D. and Tenshaw, E. and Tokhi, T. and Walsh, J.J. and Yang, T. and Horne, J.A. and Li, F. and Parekh, R. and Rivlin, P.K. and Jayaraman, V. and Ito, K. and Saalfeld, S. and George, R. and Meinertzhagen, I. and Rubin, G.M. and Hess, H.F. and Scheffer, L.K. and Jain, V. and Plaza, S.M.
bioRxiv
: 2020.01.21.911859.
21 January 2020
Apolipoprotein E4 disrupts the neuroprotective action of sortilin in neuronal lipid metabolism and endocannabinoid signaling.
Asaro, A. and Carlo-Spiewok, A.S. and Malik, A.R. and Rothe, M. and Schipke, C.G. and Peters, O. and Heeren, J. and Willnow, T.E.
bioRxiv
: 2020.01.12.903187.
14 January 2020
Concepts and software package for efficient quality control in targeted metabolomics studies - MeTaQuaC.
Kuhring, M. and Eisenberger, A. and Schmidt, V. and Kränkel, N. and Leistner, D.M. and Kirwan, J. and Beule, D.
bioRxiv
: 2020.01.10.901710.
11 January 2020
A census of cell types and paracrine interactions in colorectal cancer.
Uhlitz, F. and Bischoff, P. and Sieber, A. and Obermayer, B. and Blanc, E. and Lüthen, M. and Sawitzki, B. and Kamphues, C. and Beule, D. and Sers, C. and Horst, D. and Blüthgen, N. and Morkel, M.
bioRxiv
: 2020.01.10.901579.
11 January 2020
Dissecting the collateral damage of antibiotics on gut microbes.
Maier, L. and Goemans, C.V. and Pruteanu, M. and Wirbel, J. and Kuhn, M. and Cacace, E. and Banerjee, T. and Anderson, E.E. and Milanese, A. and Löber, U. and Forslund, S.K. and Patil, K.R. and Zeller, G. and Bork, P. and Typas, A.
bioRxiv
: 2020.01.09.893560.
9 January 2020
Exploiting a PAX3-FOXO1-induced synthetic lethal ATR dependency for rhabdomyosarcoma therapy.
García, H.D. and Bei, Y. and von Stebut, J. and Ibáñez, G. and Imami, K. and Gürgen, D. and Rolff, J. and Helmsauer, K. and Timme, N. and Bardinet, V. and Chamorro González, R. and MacArthur, I.C. and Pusch, F.F. and Chen, C.Y. and Schulz, J. and Wengner, A.M. and Furth, C. and Lala, B. and Eggert, A. and Seifert, G. and Hundsoerfer, P. and Kirchner, M. and Mertins, P. and Selbach, M. and Lissat, A. and Schulte, J.H. and Haase, K. and Scheer, M. and Ortiz, M.V. and Henssen, A.G.
bioRxiv
: 2020.12.04.411413.
2020
2019
The transcriptome dynamics of single cells during the cell cycle.
Schwabe, D. and Formichetti, S. and Junker, J.P. and Falcke, M. and Rajewsky, N.
bioRxiv
: 2019.12.23.887570.
26 December 2019
Enhancer hijacking determines intra- and extrachromosomal circular MYCN amplicon architecture in neuroblastoma.
Helmsauer, K. and Valieva, M. and Ali, S. and Chamorro González, R. and Schöpflin, R. and Röefzaad, C. and Bei, Y. and Garcia, H.D. and Rodriguez-Fos, E. and Puiggròs, M. and Kasack, K. and Haase, K. and Kuschel, L.P. and Euskirchen, P. and Heinrich, V. and Robson, M. and Rosswog, C. and Toedling, J. and Szymansky, A. and Hertwig, F. and Fischer, M. and Torrents, D. and Eggert, A. and Schulte, J.H. and Mundlos, S. and Henssen, A.G. and Koche, R.P.
bioRxiv
: 2019.12.20.875807.
20 December 2019
A novel IKK- and proteasome-independent mechanism of RelA activation triggers senescence associated secretome via transcriptional repression of NFKBIA.
Kolesnichenko, M. and Mikuda, N. and Höpken, U.E. and Milanovic, M. and Tufan, A.B. and Uyar, B. and Sun, W. and Schleich, K. and von Hoff, L. and Willenbrock, M. and Krahn, I. and Jungmann, S. and Hinz, M. and Akalin, A. and Lee, S. and Schmidt-Ullrich, R. and Schmitt, C.A. and Scheidereit, C.
bioRxiv
: 2019.12.19.882225.
20 December 2019
Histone methyltransferase DOT1L controls state-specific identity during B cell differentiation.
Aslam, M.A. and Alemdehy, M.F. and Kwesi-Maliepaard, E.M. and Caganova, M. and Pardieck, I.N. and van den Brand, T. and Muhaimin, F.I. and van Welsem, T. and de Rink, I. and Song, J.Y. and de Wit, E. and Arens, R. and Rajewsky, K. and Jacobs, H. and van Leeuwen, F.
bioRxiv
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17 December 2019
Microbiome determinants and physiological effects of the benzoate-hippurate microbial-host co-metabolic pathway.
Brial, F. and Chilloux, J. and Nielsen, T. and Vieira-Silva, S. and Falony, G. and Hoyles, L. and Neves, A.L. and Rodriguez-Martinez, A. and Mouawad, G.I. and Pons, N. and Forslund, S. and Le Chatelier, E. and Le Lay, A.M. and Nicholson, J.K. and Hansen, T. and Clément, K. and Bork, P. and Ehrlich, S.D. and Raes, J. and Pedersen, O. and Gauguier, D. and Dumas, M.E.
bioRxiv
: 2019.12.15.876672.
16 December 2019
Circuit-specific dendritic development in the piriform cortex.
Moreno-Velasquez, L. and Kaehne, M. and Lo, H. and Lenzi, S. and Breustedt, J. and Schmitz, D. and Rüdiger, S. and Johenning, F.W.
bioRxiv
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8 December 2019
Chloroplast cold-resistance is mediated by the acidic domain of the RNA binding protein CP31A.
Okuzaki, A. and Lehniger, M.K. and Muino, J.M. and Lenzen, B. and Rühe, Thilo and Leister, D. and Ohler, U. and Schmitz-Linneweber, C.
bioRxiv
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5 December 2019
LiP-Quant, an automated chemoproteomic approach to identify drug targets in complex proteomes.
Piazza, I. and Beaton, N. and Bruderer, R. and Knobloch, T. and Barbisan, C. and Siepe, I. and Rinner, O. and de Souza, N. and Picotti, P. and Reiter, L.
bioRxiv
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1 December 2019
Cross-regulation of viral kinases with cyclin A secures shutoff of host DNA synthesis.
Bogdanow, B. and Schmidt, M. and Weisbach, H. and Gruska, I. and Vetter, B. and Imami, K. and Ostermann, E. and Brune, W. and Selbach, M. and Hagemeier, C. and Wiebusch, L.
bioRxiv
: 856435.
26 November 2019
A fully phased accurate assembly of an individual human genome.
Porubsky, D. and Ebert, P. and Audano, P.A. and Vollger, M.R. and Harvey, W.T. and Munson, K.M. and Sorensen, M. and Sulovari, A. and Haukness, M. and Ghareghani, M. and Lansdorp, P.M. and Paten, B. and Devine, S.E. and Sanders, A.D. and Lee, C. and Chaisson, M.J.P. and Korbel, J.O. and Eichler, E.E. and Marschall, T.
bioRxiv
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26 November 2019
A resource of targeted mutant mouse lines for 5,061 genes.
Birling, M.C. and Yoshiki, A. and Adams, D.J. and Ayabe, S. and Beaudet, A.L. and Bottomley, J. and Bradley, A. and Brown, S.D.M. and Bürger, A. and Bushell, W. and Chiani, F. and Chin, H.J.G. and Christou, S. and Codner, G.F. and DeMayo, F.J. and Dickinson, M.E. and Doe, B. and Donahue, L.R. and Fray, M.D. and Gambadoro, A. and Gao, X. and Gertsenstein, M. and Gomez-Segura, A. and Goodwin, L.O. and Heaney, J.D. and Hérault, Y. and de Angelis, M.H. and Jiang, S.T. and Justice, M.J. and Kasparek, P. and King, R.E. and Kühn, R. and Lee, H. and Lee, Y.J. and Liu, Z. and Kent Lloyd, K.C. and Lorenzo, I. and Mallon, A.M. and McKerlie, C. and Meehan, T.F. and Newman, S. and Nutter, L.M.J. and Oh, G.T. and Pavlovic, G. and Ramirez-Solis, R. and Rosen, B. and Ryder, E.J. and Santos, L.A. and Schick, J. and Seavitt, J.R. and Sedlacek, R. and Seisenberger, C. and Seong, J.K. and Skarnes, W.C. and Sorg, T. and Steel, K.P. and Tamura, M. and Tocchini-Valentini, G.P. and Leo Wang, C.K. and Wardle-Jones, Ha. and Wattenhofer-Donzé, M. and Wells, S. and Willis, B.J. and Wood, J.A. and Wurst, W. and Xu, Y. and Teboul, L. and Murray, S.A.
bioRxiv
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22 November 2019
Single cell tri-channel-processing reveals structural variation landscapes and complex rearrangement processes.
Sanders, A.D. and Meiers, S. and Ghareghani, M. and Porubsky, D. and Jeong, H. and van Vliet, M.A.C.C. and Rausch, T. and Richter-Pechańska, P. and Kunz, J.B. and Jenni, S. and Raeder, B. and Kinanen, V. and Zimmermann, J. and Benes, V. and Schrappe, M. and Mardin, B.R. and Kulozik, A. and Bornhauser, B. and Bourquin, J.P. and Marschall, T. and Korbel, J.O.
bioRxiv
: 849604.
21 November 2019
Loss of m(1)acp(3)Ψ ribosomal RNA modification is a major feature of cancer.
Babaian, A. and Rothe, K. and Girodat, D. and Minia, I. and Djondovic, S. and Milek, M. and Wieden, H.J. and Landthaler, M. and Morin, G. and Mager, D.L.
bioRxiv
: 840132.
13 November 2019
NF1 regulates mesenchymal glioblastoma plasticity and aggressiveness through the AP-1 transcription factor FOSL1.
Marques, C. and Unterkircher, T. and Kroon, P. and Izzo, A. and Gargiulo, G. and Kling, E. and Schnell, O. and Nelander, S. and Wagner, E.F. and Bakiri, L. and Carro, M.S. and Squatrito, M.
bioRxiv
: 834531.
7 November 2019
Partner-independent fusion gene detection by multiplexed CRISPR/Cas9 enrichment and long-read Nanopore sequencing.
Stangl, C. and de Blank, S. and Renkens, I. and Verbeek, T. and Valle-Inclan, J.E. and Chamorro González, R. and Henssen, A.G. and van Roosmalen, M.J. and Stam, R.W. and Voest, E.E. and Kloosterman, W.P. and van Haaften, G. and Monroe, G.
bioRxiv
: 807545.
22 October 2019
LRP2 controls sonic hedgehog-dependent differentiation of cardiac progenitor cells during outflow tract formation.
Christ, A. and Willnow, T.E.
bioRxiv
: 801910.
11 October 2019
Predicting cellular position in the Drosophila embryo from single-cell Transcriptomics data.
Tanevski, J. and Nguyen, T. and Truong, B. and Karaiskos, N. and Ahsen, M.E. and Zhang, X. and Shu, C. and Xu, K. and Liang, X. and Hu, Y. and Pham, H.V.V. and Xiaomei, L. and Le, T.D. and Tarca, A.L. and Bhatti, G. and Romero, R. and Karathanasis, N. and Loher, P. and Chen, Y. and Ouyang, Z. and Mao, D. and Zhang, Y. and Zand, M. and Ruan, J. and Hafemeister, C. and Qiu, P. and Tran, D. and Nguyen, T. and Gabor, A. and Yu, T. and Glaab, E. and Krause, R. and Banda, P. and Stolovitzky, G. and Rajewsky, N. and Saez-Rodriguez, J. and Meyer, P.
bioRxiv
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10 October 2019
UbiFast, a rapid and deep-scale ubiquitylation profiling approach for biology and translational research.
Udeshi, N.D. and Mani, D.C. and Satpathy, S. and Fereshetian, S. and Gasser, J.A. and Svinkina, T. and Ebert, B.L. and Mertins, P. and Carr, S.A.
bioRxiv
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27 September 2019
Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation.
Dimchev, G. and Amiri, B. and Humphries, A.C. and Schaks, M. and Dimchev, V. and Stradal, T.E.B. and Faix, J. and Krause, M. and Way, M. and Falcke, M. and Rottner, K.
bioRxiv
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20 September 2019
Loss of Piccolo function in rats induces Pontocerebellar Hypoplasia type 3-like phenotypes.
Falck, J. and Bruns, C. and Hoffmann, S. and Straub, I. and Plautz, E.J. and Orlando, M. and Munawar, H. and Rivalan, M. and Winter, Y. and Izsvák, Z. and Schmitz, D. and Hamra, F.K. and Hallermann, S. and Garner, C. and Ackermann, F.
bioRxiv
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19 September 2019
Integrated proteogenomic deep sequencing and analytics accurately identify non-canonical peptides in tumor immunopeptidomes.
Chong, C. and Müller, M. and Pak, H.S. and Harnett, D. and Huber, F. and Grun, D. and Leleu, M. and Auger, A. and Arnaud, M. and Stevenson, B.J. and Michaux, J. and Bilic, I. and Hirsekorn, A. and Calviello, L. and Simó-Riudalbas, L. and Planet, E. and Lubiński, J. and Bryśkiewicz, M. and Wiznerowicz, M. and Xenarios, I. and Zhang, L. and Trono, D. and Harari, A. and Ohler, U. and Coukos, G. and Bassani-Sternberg, M.
bioRxiv
: 758680.
6 September 2019
Wnt11/Fzd7 signaling compartmentalizes AKAP2/PKA to regulate L-type Ca(2+) channel.
Csalyi, K.D. and Rharass, T. and Schulz, M. and Phan, M.H.Q. and Wakula, P. and Mhatre, K.N. and Plotnick, D. and Werdich, A.A. and Zauber, H. and Sury, M.D. and Selbach, M. and Heinzel, F.R. and Klussmann, E. and Panakova, D.
bioRxiv
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20 August 2019
Chromatin-sensitive cryptic promoters encode alternative protein isoforms in yeast.
Wei, W. and Hennig, B.P. and Wang, J. and Zhang, Y. and Piazza, I. and Sanchez, Y.P. and Chabbert, C.D. and Adjalley, S.H. and Steinmetz, L.M. and Pelechano, V.
bioRxiv
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12 August 2019
Maximizing binary interactome mapping with a minimal number of assays.
Choi, S.G. and Olivet, J. and Cassonnet, P. and Vidalain, P.O. and Luck, K. and Lambourne, L. and Spirohn, K. and Lemmens, I. and Dos Santos, M. and Demeret, C. and Jones, L. and Rangarajan, S. and Bian, W. and Coutant, E.P. and Janin, Y.L. and van der Werf, S. and Trepte, P. and Wanker, E.E. and De Las Rivas, J. and Tavernier, J. and Twizere, J.C. and Hao, T. and Hill, D.E. and Vidal, M. and Calderwood, M.A. and Jacob, Y.
bioRxiv
: 530790.
9 August 2019
Human endogenous retrovirus HERV-K(HML-2) RNA causes neurodegeneration through Toll-like receptors.
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bioRxiv
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1 August 2019
WiPP: workflow for improved peak picking for gas chromatography-mass spectrometry (GC-MS) data.
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bioRxiv
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24 July 2019
SCelVis: Powerful explorative single cell data analysis on the desktop and in the cloud.
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bioRxiv
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24 July 2019
Functional annotation of human long non-coding RNAs via molecular phenotyping.
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18 July 2019
Janggu: deep learning for genomics.
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16 July 2019
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28 June 2019
Stochastic transcription in the p53-mediated response to DNA damage is modulated by burst frequency.
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bioRxiv
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21 June 2019
Low-density granulocytes are a novel immunopathological feature in both multiple sclerosis and neuromyelitis optica spectrum disorder.
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12 June 2019
Identification of TMEM206 proteins as pore of ASOR acid-sensitive chloride channels.
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bioRxiv
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11 June 2019
A helminth chitinase structurally similar to mammalian chitinase displays immunomodulatory properties.
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17 May 2019
Inter-individual and inter-strain differences in cognitive and social abilities of Dark Agouti and Wistar Han rats.
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23 April 2019
SaTAnn quantifies translation on the functionally heterogeneous transcriptome.
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14 April 2019
Integrative functional genomics decodes herpes simplex virus 1.
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bioRxiv
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9 April 2019
Ribo-seQC: comprehensive analysis of cytoplasmic and organellar ribosome profiling data.
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8 April 2019
Codon bias confers stability to mRNAs via ILF2 in humans.
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4 April 2019
Distinct immune evasion in APOBEC-enriched, HPV-negative HNSCC.
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28 March 2019
DDX3 depletion selectively represses translation of structured mRNAs.
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26 March 2019
Prediction of combination therapies based on topological modeling of the immune signaling network in multiple sclerosis.
Bernardo-Faura, M. and Rinas, M. and Wirbel, J. and Pertsovskaya, I. and Pliaka, V. and Messinis, D.E and Vila, G. and Sakellaropoulos, T. and Faigle, W. and Stridh, P. and Behrens, J.R. and Olsson, T. and Martin, R. and Paul, F. and Alexopoulos, L.G. and Villoslada, P. and Saez-Rodriguez, J.
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20 March 2019
A quantitative modular modeling approach reveals the consequences of different A20 feedback implementations for the NF-κB signaling dynamics.
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19 March 2019
Endothelial PKA targets ATG16L1 to regulate angiogenesis by limiting autophagy.
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bioRxiv
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12 March 2019
EHD2-mediated restriction of caveolar dynamics regulates cellular lipid uptake.
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7 March 2019
Single-cell RNA-sequencing of Herpes simplex virus 1-infected cells identifies NRF2 activation as an antiviral program.
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4 March 2019
The Tug1 locus is essential for male fertility.
Lewandowski, J.P. and Dumbović, G. and Watson, A.R. and Hwang, T. and Jacobs-Palmer, E. and Chang, N. and Much, C. and Turner, K. and Kirby, C. and Schulz, J.F. and Müller, C.L. and Rubinstein, N.D. and Groff, A.F. and Liapis, S.C. and Gerhardinger, C. and Hubner, N. and van Heesch, S. and Hoekstra, H.E. and Sauvageau, M. and Rinn, J.L.
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28 February 2019
BIQ: A method for searching circular RNAs in transcriptome databases by indexing backsplice junctions.
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bioRxiv
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25 February 2019
Crowdfunded whole-genome sequencing of the celebrity cat Lil BUB identifies causal mutations for her osteopetrosis and polydactyly.
Bridavsky, M. and Kuhl, H. and Woodruf, A. and Kornak, U. and Timmermann, B. and Mages, N. and Lupiáñez, D.G. and Symmons, O. and Ibrahim, D.M.
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22 February 2019
SURF1 mutations causative of Leigh syndrome impair human neurogenesis.
Inak, G. and Rybak-Wolf, A. and Lisowski, P. and Juettner, R. and Zink, A. and Mlody, B. and Glazar, P. and Secker, C. and Ciptasari, U.H. and Stenzel, W. and Hahn, T. and Diecke, S. and Priller, J. and Gotthardt, M. and Kuehn, R. and Wanker, E.E. and Rajewsky, N. and Schuelke, M. and Prigione, A.
bioRxiv
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20 February 2019
Full-length mRNA sequencing reveals principles of poly(A) tail length control.
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bioRxiv
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11 February 2019
The conserved histone chaperone LIN-53 links lifespan and healthspan regulation in C. elegans.
Müthel, S. and Uyar, B. and He, M. and Krause, A. and Vitrinel, B. and Bulut, S. and Vasiljevic, D. and Akalin, A. and Kempa, S. and Tursun, B.
bioRxiv
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2 February 2019
Deep neural networks for interpreting RNA binding protein target preferences.
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bioRxiv
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11 January 2019
Splicing factor Rbm10 facilitates heterochromatin assembly in fission yeast.
Weigt, M. and Gao, Q. and Ban, H. and He, H. and Mastrobuoni, G. and Kempa, S. and Chen, W. and Li, F.
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11 January 2019
Multiple two-photon targeted whole-cell patch-clamp recordings from monosynaptically connected neurons in vivo.
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9 January 2019
2018
Prohibitin is a prognostic marker of relapse and therapeutic target to block chemotherapy resistance in Wilms tumor.
Ortiz, M.V. and Ahmed, S. and Burns, M. and Henssen, A.G. and Hollmann, T.J. and MacArthur, I. and Gunasekera, S. and Gaewsky, L. and Bradwin, G. and Ryan, J. and Letai, A. and He, Y. and Naranjo, A. and Chi, Y.Y. and LaQuaglia, M. and Heaton, T. and Cifani, P. and Dome, J.S. and Gadd, S. and Perlman, El. and Mullen, E. and Steen, H. and Kentsis, A.
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30 December 2018
A gene expression atlas of embryonic neurogenesis in Drosophila reveals complex spatiotemporal regulation of lncRNAs.
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27 December 2018
The sensory coding of warm perception: supplementary figures.
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20 December 2018
A novel non-invasive method to detect gut barrier related changes during a gastrointestinal nematode infection.
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17 December 2018
Targeted genomic integration of EGFP under tubulin beta 3 class III promoter and mEos2 under tryptophan hydroxylase 2 promoter does not produce sufficient levels of reporter gene expression.
Menzorov, A.G. and Orishchenko, K. and Fishman, V. and Shevtsova, A. and Mungalov, R. and Pristyazhnyuk, I. and Kizilova, E. and Matveeva, N. and Alenina, N. and Bader, M. and Rubtsov, N. and Serov, O.
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7 December 2018
DeepWAS: Multivariate genotype-phenotype associations by directly integrating regulatory information using deep learning.
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5 December 2018
RIM-BP2 primes synaptic vesicles via recruitment of Munc13-1 at hippocampal mossy fiber synapses.
Brockmann, M.M. and Maglione, M. and Willmes, C.G. and Stumpf, A. and Bouazza, B.A. and Velasquez, L.M. and Grauel, M.K. and Beed, P. and Sigrist, S.J. and Rosenmund, C. and Schmitz, D.
bioRxiv
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13 November 2018
Evaluation of colorectal cancer subtypes and cell lines using deep learning.
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12 November 2018
Glutamate uptake and release at single adult corticostriatal synapses of normal and Huntington mice.
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bioRxiv
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30 October 2018
Charting a tissue from single-cell transcriptomes.
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30 October 2018
Translational control of cardiac fibrosis.
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24 October 2018
The dynamic proteome of influenza A virus infection identifies M segment splicing as a host range determinant.
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bioRxiv
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8 October 2018
Emergence of robust nucleosome patterns from an interplay of positioning mechanisms.
Nuebler, J. and Wolff, M. and Obermayer, B. and Mobius, W. and Gerland, U.
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1 October 2018
SorCS2 controls functional expression of amino acid transporter EAAT3 to protect neurons from oxidative stress and epilepsy-induced pathology.
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25 September 2018
MYCN-induced metabolic rewiring creates novel therapeutic vulnerabilities in neuroblastoma.
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25 September 2018
Mutant screen reveals the Piccolo's control over depression and brain-gonad crosstalk.
Medrano, G.A. and Singh, M. and Plautz, E.J. and Good, L.B. and Chapman, K.M. and Chaudhary, J. and Jaichander, P. and Powell, H.M. and Pudasaini, A. and Shelton, J.M. and Richardson, J.A. and Xie, X.J. and Ivics, Z. and Braun, C. and Ackermann, F. and Garner, C.C. and Izsvak, Z. and Hamra, F.K.
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31 August 2018
Profound functional and molecular diversity of mitochondria revealed by cell type-specific profiling in vivo.
Fecher, C. and Trovò, L. and Müller, S.A. and Snaidero, N. and Wettmarshausen, J. and Heink, S. and Ortiz, O. and Wagner, I. and Kühn, R. and Hartmann, J. and Karl, R.M. and Konnerth, A. and Korn, T. and Wurst, W. and Merkler, D. and Lichtenthaler, S.L. and Perocchi, F. and Misgeld, T.
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29 August 2018
Arterio-venous remodeling in the zebrafish trunk is controlled by genetic programming and flow-mediated fine-tuning.
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29 August 2018
Spatial organization of Rho GTPase signaling by RhoGEF/RhoGAP proteins.
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29 August 2018
Global identification of functional microRNA::mRNA interactions in Drosophila.
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22 August 2018
Identification and ranking of recurrent neo-epitopes in cancer.
Blanc, E. and Holtgrewe, M. and Dhamodaran, A. and Messerschmidt, C. and Willimsky, G. and Blankenstein, T. and Beule, D.
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10 August 2018
MTrack: automated detection, tracking, and analysis of dynamic microtubules.
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13 July 2018
Long non-coding RNAs defining major subtypes of B cell precursor acute lymphoblastic leukemia.
Rani James, A. and Schroeder, M.P. and Neumann, M. and Bastian, L. and Eckert, C. and Gökbuget, N. and Tanchez, J.O. and Schlee, C. and Isaakidis, K. and Schwartz, S. and Burmeister, T. and von Stackelberg, A. and Rieger, M.A. and Göllner, S. and Horstman, M. and Schrappe, M. and Kirschner-Schwabe, R. and Brüggemann, M. and Müller-Tidow, C. and Serve, H. and Akalin, A. and Baldus, C.D.
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9 July 2018
Single-cell transcriptomics characterizes cell types in the subventricular zone and uncovers molecular defects underlying impaired adult neurogenesis.
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9 July 2018
VGLUT2 functions as a differential marker for hippocampal output neurons.
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17 June 2018
Regulation of spatial and temporal gene expression in an animal germline.
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15 June 2018
Spatial transcriptomics of C. elegans males and hermaphrodites identifies novel fertility genes.
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15 June 2018
BigStitcher: Reconstructing high-resolution image datasets of cleared and expanded samples.
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10 June 2018
Chromatin accessibility is dynamically regulated across C. elegans development and ageing.
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10 June 2018
Specialized mechanoreceptor systems in rodent glabrous skin.
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5 June 2018
Loss of the Wnt/β-catenin pathway in microglia of the developing brain drives pro-inflammatory activation leading to white matter injury.
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31 May 2018
Purification of cross-linked RNA-protein complexes by phenol-toluol extraction.
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30 May 2018
Critical role for Piccolo in synaptic vesicle retrieval.
Ackermann, F. and Schink, K.O. and Bruns, C. and Izsvak, Z. and Hamra, K. and Rosenmund, C. and Garner, C.C.
bioRxiv
: 330050.
24 May 2018
The phylogenetically distinct early human embryo.
Singh, M. and Widmann, T.J. and Cortes, J.L. and Schumann, G.G. and Wunderlich, S. and Martin, U. and Garcia-Perez, J.L. and Hurst, L.D. and Izsvak, Z.
bioRxiv
: 318329.
18 May 2018
Estrus-cycle regulation of cortical inhibition.
Clemens, A.M. and Lenschow, C. and Beed, P. and Li, L. and Sammons, R. and Naumann, R.K. and Wang, H. and Schmitz, D. and Brecht, M.
bioRxiv
: 314641.
5 May 2018
Quantifying multi-layered expression regulation in response to stress of the endoplasmic reticulum.
Rendleman, J. and Cheng, Z. and Maity, S. and Kastelic, N. and Munschauer, M. and Allgoewer, K. and Teo, G. and Zhang, Y.B. and Lei, A. and Parker, B. and Landthaler, M. and Freeberg, L. and Kuersten, S. and Choi, H. and Vogel, C.
bioRxiv
: 308379.
25 April 2018
Reproducible genomics analysis pipelines with GNU Guix.
Wurmus, R. and Uyar, B. and Osberg, B. and Franke, V. and Gosdschan, A. and Wreczycka, K. and Ronen, J. and Akalin, A.
bioRxiv
: 298653.
21 April 2018
Deciphering human ribonucleoprotein regulatory networks.
Mukherjee, N. and Wessels, H.H. and Lebedeva, S. and Sajek, M. and Ghanbari, M. and Garzia, A. and Munteanu, A. and Farazi, T. and Hoell, J.I. and Akat, K. and Tuschl, T. and Ohler, U.
bioRxiv
: 295097.
10 April 2018
Cumulative regulatory potential of clustered methyl-arginine protein modifications.
Woodsmith, J. and Casado-Medrano, V. and Benlasfer, N. and Eccles, R.L. and Hutten, S. and Heine, C. and Thormann, V. and Abou-Ajram, C. and Rocks, O. and Dormann, D. and Stelzl, U.
bioRxiv
: 289041.
26 March 2018
Low frequency and rare coding variation contributes to multiple sclerosis risk.
bioRxiv
: 286617.
23 March 2018
SSMART: Sequence-structure motif identification for RNA-binding proteins.
Munteanu, A. and Mukherjee, N. and Ohler, U.
bioRxiv
: 287953.
23 March 2018
Reproducible inference of transcription factor footprints in ATAC-seq and DNase-seq datasets via protocol-specific bias modeling.
Karabacak Calviello, A. and Hirsekorn, A. and Wurmus, R. and Yusuf, D. and Ohler, U.
bioRxiv
: 284364.
19 March 2018
Mutant Plasticity Related Gene 1 (PRG1) acts as a potential modifier in SCN1A related epilepsy.
Knierim, E. and Vogt, J. and Kintscher, M. and Ponomarenko, A. and Baumgart, J. and Sanker Beed, P. and Korotkova, T. and Trimbuch, T. and Panzer, A. and Stephani, U. and Escayg, A. and Lerche, H. and Nitsch, R. and Schmitz, D. and Schuelke, M.
bioRxiv
: 282871.
15 March 2018
Genomic basis for RNA alterations revealed by whole-genome analyses of 27 cancer types.
Calabrese, C. and Davidson, N.R. and Fonseca, N.A. and He, Y. and Kahles, A. and Lehmann, K.V. and Liu, F. and Shiraishi, Y. and Soulette, C.M. and Urban, L. and Demircioğlu, D. and Greger, L. and Li, S. and Liu, D. and Perry, M.D. and Xiang, L. and Zhang, F. and Zhang, J. and Bailey, P. and Erkek, S. and Hoadley, K.A. and Hou, Y. and Kilpinen, H. and Korbel, J.O. and Marin, M.G. and Markowski, J. and Nandi, T. and Pan-Hammarström, Q. and Pedamallu, C.S. and Siebert, R. and Stark, S.G. and Su, H. and Tan, P. and Waszak, S.M. and Yung, C. and Zhu, S. and Awadalla, P. and Creighton, C.J. and Meyerson, M. and Ouellette, B.F.F. and Wu, K. and Yang, H. and Brazma, A. and Brooks, A.N. and Göke, J. and Rätsch, G. and Schwarz, R.F. and Stegle, O. and Zhang, Z.
bioRxiv
: 183889.
12 March 2018
Kinetic modelling of quantitative proteome data predicts metabolic reprogramming of liver cancer.
Berndt, N. and Egners, A. and Mastrobuoni, G. and Vvedenskaya, O. and Fragoulis, A. and Dugourd, A. and Bulik, S. and Pietzke, M. and Bielow, C. and van Gassel, R. and Olde Damink, S. and Erdem, M. and Saez-Rodriguez, J. and Holzhütter, H.G. and Kempa, S. and Cramer, T.
bioRxiv
: 275040.
5 March 2018
Non-canonical HIF-1 stabilization is essential for intestinal tumorigenesis.
Rohwer, N. and Jumpertz, S. and Erdem, M. and Egners, A. and Warzecha, K.T. and Fragoulis, A. and Kuehl, A.A. and Kramann, R. and Neuss, S. and Rudolph, I. and Endermann, T. and Zasada, C. and Apostolova, I. and Gerling, M. and Kempa, S. and Hughes, R. and Lewis, C.E. and Brenner, W. and Malinowski, M.B. and Stockmann, M. and Schomburg, L. and Faller, W. and Sansom, O.J. and Tacke, F. and Morkel, M. and Cramer, T.
bioRxiv
: 273045.
28 February 2018
Human axial progenitors generate trunk neural crest cells.
Frith, T.J.R. and Granata, I. and Stout, E. and Wind, M. and Thompson, O. and Neumann, K. and Stavish, D. and Heath, P.R. and Hackland, J.O.S. and Anastassiadis, K. and Gouti, M. and Briscoe, J. and Wilson, V. and Guarracino, M.R. and Andrews, P.W. and Tsakiridis, A.
bioRxiv
: 272591.
27 February 2018
An eicosanoid protects from statin-induced myopathic changes in primary human cells.
Grunwald, S.A. and Popp, O. and Haafke, S. and Jedraszczak, N. and Grieben, U. and Saar, K. and Patone, G. and Kress, W. and Steinhagen-Thiessen, E. and Dittmar, G. and Spuler, S.
bioRxiv
: 271932.
26 February 2018
Construction of whole genomes from scaffolds using single cell strand-seq data.
Hills, M. and Falconer, E. and O’Neil, K. and Sanders, A.D. and Howe, K. and Guryev, V. and Lansdorp, P.M.
bioRxiv
: 271510.
26 February 2018
Proteomic analysis of chemosensory organs in the honey bee parasite Varroa destructor: a comprehensive examination of the potential carriers for semiochemicals.
Iovinella, I. and McAfee, A. and Mastrobuoni, G. and Kempa, S. and Foster, L.J. and Pelosi, P. and Dani, F.R.
bioRxiv
: 260539.
7 February 2018
2017
Visualization of class A GPCR oligomerization by image-based fluorescence fluctuation spectroscopy.
Isbilir, A. and Moeller, J. and Bock, A. and Zabel, U. and Annibale, P. and Lohse, M.J.
bioRxiv
: 240903.
29 December 2017
PolNet Analysis: a software tool for the quantification of network-level endothelial cell polarity and blood flow during vascular remodelling.
Bernabeu, M.O. and Jones, M.L. and Nash, R.W. and Pezzarossa, A. and Coveney, P.V. and Gerhardt, H. and Franco, C.A.
bioRxiv
: 237602.
22 December 2017
Protein Interaction Screen on Peptide Matrix (PRISMA) reveals interaction footprints and the PTM-dependent interactome of intrinsically disordered C/EBPβ.
Dittmar, G. and Perez-Hernandez, D. and Kowenz-Leutz, E. and Kirchner, M. and Kahlert, G. and Wesolowski, R. and Baum, K. and Knoblich, M. and Muller, A. and Wolf, J. and Reimer, U. and Leutz, A.
bioRxiv
: 238709.
22 December 2017
Reliable detection of translational regulation with Ribo-seq.
Chothani, S.P. and Adami, E. and Viswanathan, S. and Hubner, N. and Cook, S. and Schafer, S. and Rackham, O.J.L.
bioRxiv
: 234344.
15 December 2017
netSmooth: Network-smoothing based imputation for single cell RNA-seq.
Ronen, J. and Akalin, A.
bioRxiv
: 234021.
13 December 2017
Continuous addition of progenitors forms the cardiac ventricle in zebrafish.
Felker, A. and Prummel, K.D. and Merks, A.M. and Mickoleit, M. and Brombacher, E.C. and Huisken, J. and Panakova, D. and Mosimann, C.
bioRxiv
: 230649.
7 December 2017
Evolutionary plasticity in the innate immune function of Akirin.
Polanowska, J. and Chen, J.X. and Soule, J. and Omi, S. and Belougne, J. and Taffoni, C. and Pujol, N. and Selbach, M. and Zugasti, O. and Ewbank, J.J.
bioRxiv
: 230102.
6 December 2017
Regionalization of the nervous system requires axial allocation prior to neural lineage commitment.
Metzis, V. and Steinhauser, S. and Pakanavicius, E. and Gouti, M. and Stamataki, D. and Lovell-Badge, R. and Luscombe, N.M. and Briscoe, J.
bioRxiv
: 229203.
4 December 2017
Assessing the gene regulatory landscape in 1,188 human tumors.
Calabrese, C. and Lehmann, K.V. and Urban, L. and Liu, F. and Erkek, S. and Fonseca, N. and Kahles, A. and Kilpinen-Barrett, L.H. and Markowski, J. and Waszak, S. and Korbel, J. and Zhang, Z. and Brazma, A. and Raetsch, G. and Schwarz, R. and Stegle, O.
bioRxiv
: 225441.
29 November 2017
Determinants of transcription initiation directionality in metazoans.
Ibrahim, M.M. and Karabacak, A. and Glahs, A. and Kolundzic, E. and Hirsekorn, A. and Carda, A. and Tursun, B. and Zinzen, R.P. and Lacadie, S.A. and Ohler, U.
bioRxiv
: 224642.
24 November 2017
B-1a cells acquire their unique characteristics by bypassing the pre-BCR selection stage.
Wong, J.B. and Hewitt, S.L. and Heltemes-Harris, L.M. and Mandal, M. and Johnson, K. and Rajewsky, K. and Koralov, S.B. and Clark, M.R. and Farrar, M.A. and Skok, J.A.
bioRxiv
: 214908.
13 November 2017
Germline determinants of the somatic mutation landscape in 2,642 cancer genomes.
Waszak, S.M. and Tiao, G. and Zhu, B. and Rausch, T. and Muyas, F. and Rodriguez-Martin, B. and Rabionet, R. and Yakneen, S. and Escaramis, G. and Li, Y. and Saini, N. and Roberts, S.A. and Demidov, G.M. and Pitkanen, E. and Delaneau, O. and Heredia-Genestar, J.M. and Weischenfeldt, J. and Shringarpure, S.S. and Chen, J. and Nakagawa, H. and Alexandrov, L.B. and Drechsel, O. and Dursi, L.J. and Segre, A.V. and Garrison, E. and Erkek, S. and Habermann, N. and Urban, L. and Khurana, E. and Cafferkey, A. and Hayashi, S. and Imoto, S. and Aaltonen, L.A. and Alvarez, E.G. and Baez-Ortega, A. and Bailey, M. and Bosio, M. and Bruzos, A.L. and Buchhalter, I. and Bustamante, C.D. and Calabrese, C. and DiBiase, A. and Gerstein, M. and Holik, A.Z. and Hua, X. and Huang, K.l. and Letunic, I. and Klimczak, L.J. and Koster, R. and Kumar, S. and McLellan, M. and Mashl, J. and Mirabello, L. and Newhouse, S. and Prasad, A. and Raetsch, G. and Schlesner, M. and Schwarz, R. and Sharma, P. and Shmaya, T. and Sidiropoulos, N. and Song, L. and Susak, H. and Tanskanen, T. and Tojo, M. and Wedge, D.C. and Wright, M. and Wu, Y. and Ye, K. and Yellapantula, V. D. and Zamora, J. and Butte, A.J. and Getz, G. and Simpson, J. and Ding, L. and Marques-Bonet, T. and Navarro, A. and Brazma, A. and Campbell, P. and Chanock, S.J. and Chatterjee, N. and Stegle, O. and Siebert, R. and Ossowski, S. and Harismendy, O. and Gordenin, D.A. and Tubio, J.M.C. and De La Vega, F.M. and Easton, D.F. and Estivill, X. and Korbel, J.
bioRxiv
: 208330.
1 November 2017
Graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells.
Wolf, F.A. and Hamey, F. and Plass, M. and Solana, J. and Dahlin, J.S. and Gottgens, B. and Rajewsky, N. and Simon, L. and Theis, F.J.
bioRxiv
: 208819.
25 October 2017
No major flaws in "Identification of individuals by trait prediction using whole-genome sequencing data".
Lippert, C. and Sabatini, R. and Maher, M.C. and Kang, E.Y. and Lee, S. and Arikan, O. and Harley, A. and Bernal, A. and Garst, P. and Lavrenko, V. and Yocum, K. and Wong, T.M. and Zhu, M. and Yang, W.Y.n and Chang, C. and Hicks, B. and Ramakrishnan, S. and Tang, H. and Xie, C. and Brewerton, S. and Turpaz, Y. and Telenti, A. and Roby, R.K. and Och, F. and Venter, J.C.
bioRxiv
: 187542.
19 October 2017
Massively parallel single cell lineage tracing using CRISPR/Cas9 induced genetic scars.
Spanjaard, B. and Hu, B. and Mitic, N. and Junker, J.P.
bioRxiv
: 205971.
19 October 2017
Fibril branching dominates self-assembly of mutant huntingtin exon-1 aggregates in vitro.
Wagner, A.S. and Politi, A.Z. and Steinhof, A. and Bravo-Rodriguez, K. and Buntru, A. and Strempel, N.U. and Brusendorf, L. and Haenig, C. and Boeddrich, A. and Plassmann, S. and Ramirez-Anguita, J.M. and Baum, K. and Sanchez-Garcia, E. and Wolf, J. and Wanker, E.E.
bioRxiv
: 195297.
19 October 2017
Picky: a simple method designer for targeted proteomics.
Zauber, H. and Kirchner, M. and Selbach, M.
bioRxiv
: 163154.
6 October 2017
Defective synapse maturation and enhanced synaptic plasticity in Shank2(-/-) mice.
Wegener, S. and Buschler, A. and Stempel, A.V. and Shoichet, S.A. and Manahan-Vaughan, D. and Schmitz, D.
bioRxiv
: 193078.
29 September 2017
FACT sets a barrier for cell fate reprogramming in C. elegans and human.
Kolundzic, E. and Ofenbauer, A. and Uyar, B. and Sommermeier, A. and Seelk, S. and He, M. and Baytek, G. and Akalin, A. and Diecke, S. and Lacadie, S.A. and Tursun, B.
bioRxiv
: 185116.
6 September 2017
Therapeutic targeting of PGBD5-induced DNA repair dependency in pediatric solid tumors.
Henssen, A.G. and Reed, Casie and Jiang, Eileen and Garcia, H.D. and von Stebut, J. and MacArthur, I.C. and Hundsdoerfer, P. and Kim, J.H. and de Stanchina, E. and Kuwahara, Y. and Hosoi, H. and Ganem, N. and Cruz, F.D. and Kung, A.L. and Schulte, J.H. and Petrini, J.H. and Kentsis, A.
bioRxiv
: 181040.
25 August 2017
De novo mutations implicate novel genes with burden of rare variants in systemic lupus erythematosus.
Pullabhatla, V. and Roberts, A.L. and Lewis, M.J. and Mauro, D. and Morris, D.L. and Odhams, C.A. and Tombleson, P. and Liljedahld, U. and Vyse, S. and Simpson, M.A. and Sauer, S. and de Rinaldis, E. and Syvaenen, A.C. and Vyse, T.J.
bioRxiv
: 139238.
14 August 2017
YAP and TAZ regulate adherens junction dynamics and endothelial cell distribution during vascular development.
Neto, F. and Klaus-Bergmann, A. and Ong, Y.T. and Alt, S. and Vion, A.C. and Szymborska, A. and Carvalho, J.R. and Hollfinger, I. and Bartels-Klein, E. and Franco, C.A. and Potente, M. and Gerhardt, H.
bioRxiv
: 174185.
9 August 2017
Strategies for analyzing bisulfite sequencing data.
Wreczycka, K. and Gosdschan, A. and Yusuf, D. and Gruening, B. and Assenov, Y. and Akalin, A.
bioRxiv
: 109512.
9 August 2017
HOT or not: Examining the basis of high-occupancy target regions.
Wreczycka, K. and Franke, V. and Uyar, B. and Wurmus, R. and Akalin, A.
bioRxiv
: 107680.
31 July 2017
Correcting batch effects in single-cell RNA sequencing data by matching mutual nearest neighbours.
Haghverdi, L. and Lun, A.T.L. and Morgan, M.D. and Marioni, J.C.
bioRxiv
: 165118.
18 July 2017
omniCLIP: Bayesian identification of protein-RNA interactions from CLIP-Seq data.
Drewe-Boss, P. and Wessels, H.H. and Ohler, U.
bioRxiv
: 161877.
11 July 2017
Voltage-gating of mechanosensitive PIEZO channels.
Moroni, M. and Servin-Vences, M.R. and Fleischer, R. and Lewin, G.R.
bioRxiv
: 156489.
27 June 2017
Mutations in disordered regions cause disease by creating endocytosis motifs.
Meyer, K. and Uyar, B. and Kirchner, M. and Cheng, J. and Akalin, A. and Selbach, M.
bioRxiv
: 141622.
24 May 2017
Cell dynamics underlying oriented growth of the Drosophila wing imaginal disc.
Dye, N.A. and Popovic, M. and Spannl, S. and Etournay, R. and Kainmueller, D. and Myers, E.W. and Julicher, F. and Eaton, S.
bioRxiv
: 140038.
19 May 2017
Neuronal inhibition of the autophagy nucleation complex extends lifespan in post-reproductive C. elegans.
Wilhelm, T. and Byrne, J. and Medina, R. and Kolundzic, E. and Geisinger, J. and Hajduskova, M. and Tursun, B. and Richly, H.
bioRxiv
: 135178.
8 May 2017
Cell fixation and preservation for droplet-based single-cell transcriptomics.
Alles, J. and Karaiskos, N. and Praktiknjo, S. and Grosswendt, S. and Wahle, P. and Ruffault, P.L. and Ayoub, S. and Schreyer, L. and Boltengagen, A. and Birchmeier, C. and Zinzen, R. and Kocks, C. and Rajewsky, N.
bioRxiv
: 099473.
13 April 2017
GAMtools: an automated pipeline for analysis of Genome Architecture Mapping data.
Beagrie, R.A. and Schueler, M.
bioRxiv
: 114710.
20 March 2017
The Drosophila embryo at single cell transcriptome resolution.
Karaiskos, N. and Wahle, P. and Alles, J. and Boltengagen, A. and Ayoub, S. and Kipar, C. and Kocks, C. and Rajewsky, N. and Zinzen, R.P.
bioRxiv
: 117382.
17 March 2017
Flipping between Polycomb repressed and active transcriptional states introduces noise in gene expression.
Kar, G. and Kim, J.K. and Kolodziejczyk, A.A. and Natarajan, K.N. and Torlai Triglia, E. and Mifsud, B. and Elderkin, S. and Marioni, J.C. and Pombo, A. and Teichmann, S.A.
bioRxiv
: 117267.
16 March 2017
Active and poised promoter states drive folding of the extended HoxB locus in mouse embryonic stem cells.
Barbieri, M. and Xie, S.Q. and Torlai Triglia, E. and de Santiago, I. and Branco, M.R. and Rueda, D. and Nicodemi, M. and Pombo, A.
bioRxiv
: 111773.
28 February 2017
Reconstruction of cell lineages and behaviors underlying arthropod limb outgrowth with multi-view light-sheet imaging and tracking.
Wolff, C. and Tinevez, J.Y. and Pietzsch, T. and Stamataki, E. and Harich, B. and Preibisch, S. and Shorte, S. and Keller, P.J. and Tomancak, P. and Pavlopoulos, A.
bioRxiv
: 112623.
28 February 2017
Human PGBD5 DNA transposase promotes site-specific oncogenic mutations in rhabdoid tumors.
Henssen, A.G. and Koche, R. and Zhuang, J. and Jiang, E. and Reed, C. and Eisenberg, A. and Still, E. and MacArthur, I.C. and Rodriguez-Fos, E. and Gonzalez, S. and Puiggròs, M. and Blackford, A.N. and Mason, C.E. and de Stanchina, E. and Gönen, M. and Emde, An.K. and Shah, M. and Arora, K. and Reeves, C. and Socci, N.D. and Perlman, E. and Antonescu, C.R. and Roberts, C.W.M. and Steen, H. and Mullen, E. and Jackson, S.P. and Torrents, D. and Weng, Z. and Armstrong, S.A. and Kentsis, A.
bioRxiv
: 111138.
23 February 2017
Massively parallel clonal analysis using CRISPR/Cas9 induced genetic scars.
Junker, J.P. and Spanjaard, B. and Peterson-Maduro, J. and Alemany, A. and Hu, B. and Florescu, M. and van Oudenaarden, A.
bioRxiv
: 056499.
4 January 2017
2016
Excitability in the p53 network mediates robust signaling with tunable activation thresholds in single cells.
Moenke, G. and Cristiano, E. and Finzel, A. and Friedrich, D. and Herzel, H. and Falcke, M. and Loewer, A.
bioRxiv
: 068668.
28 November 2016
Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction.
Schmidt, F. and Gasparoni, N. and Gasparoni, G. and Gianmoena, K. and Cadenas, C. and Polansky, J.K. and Ebert, P. and Nordstroem, K. and Barann, M. and Sinha, A. and Froehler, S. and Xiong, J. and Amirabad, A.D. and Ardakani, F.B. and Hutter, B. and Zipprich, G. and Felder, B. and Eils, J. and Brors, B. and Chen, W. and Hengstler, J.G. and Hamann, A. and Lengauer, T. and Rosenstiel, P. and Walter, J. and Schulz, M.H.
bioRxiv
: 081935.
19 October 2016
ssHMM: Extracting intuitive sequence-structure motifs from high-throughput RNA-binding protein data.
Heller, D. and Krestel, R. and Ohler, U. and Vingron, M. and Marsico, A.
bioRxiv
: 076034.
11 October 2016
Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper.
Huerta-Cepas, J. and Forslund, K. and Szklarczyk, D. and Jensen, L.J. and von Mering, C. and Bork, P.
bioRxiv
: 076331.
22 September 2016
Integrative classification of human coding and non-coding genes based on RNA metabolism profiles.
Mukherjee, N. and Calviello, L. and Hirsekorn, A. and de Pretis, S. and Pelizzola, M. and Ohler, U.
bioRxiv
: 073643.
6 September 2016
HLA-MA: Simple yet powerful matching of samples using HLA typing results.
Messerschmidt, C. and Holtgrewe, M. and Beule, D.
bioRxiv
: 066548.
24 August 2016
Forward genetic screen of human transposase genomic rearrangements.
Henssen, A.G. and Jiang, E. and Zhuang, J. and Pinello, L. and Socci, N.D. and Koche, R. and Gonen, M. and Villasante, C.M. and Armstrong, S.A. and Bauer, D.E. and Weng, Z. and Kentsis, A.
bioRxiv
: 061770.
1 July 2016
Ecogenomics and biogeochemical impacts of uncultivated globally abundant ocean viruses.
Roux, S. and Brum, J.R. and Dutilh, B.E. and Sunagawa, S. and Duhaime, M.B. and Loy, A. and Poulos, B.T. and Solonenko, N. and Lara, E. and Poulain, J. and Pesant, S. and Kandels-Lewis, S. and Dimier, C. and Picheral, M. and Searson, S. and Cruaud, C. and Alberti, A. and Duarte, C.M. and Gasol, J.M. and Vaque, D. and Bork, P. and Acinas, S.G. and Wincker, P. and Sullivan, M.B.
bioRxiv
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12 May 2016
Hormetic shifting of redox environment by pro-oxidative resveratrol protects cells against stress.
Plauth, A. and Geikowski, A. and Cichon, S. and Wowro, S.J. and Liedgens, L. and Rousseau, M. and Weidner, C. and Fuhr, L. and Kliem, M. and Jenkins, G. and Lotito, S. and Wainwright, L.J. and Sauer, S.
bioRxiv
: 045567.
24 March 2016
Diffusion pseudotime robustly reconstructs lineage branching.
Haghverdi, L. and Büttner, M. and Wolf, F. A. and Buettner, F. and Theis, F.J.
bioRxiv
: 041384.
2 March 2016
RiboDiff: detecting changes of translation efficiency from ribosome footprints.
Zhong, Y. and Karaletsos, T. and Drewe, P. and Sreedharan, V. and Kuo, D. and Singh, K. and Wendel, H.G. and Raetsch, G.
bioRxiv
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11 January 2016
2015
Differential dynamics of the mammalian mRNA and protein expression response to misfolding stress.
Cheng, Z. and Teo, G. and Krueger, S. and Rock, T. and Koh, H.W.L. and Choi, H. and Vogel, C.
bioRxiv
: 032797.
26 November 2015
G-quadruplex prediction in E.coli genome reveals a conserved putative G-quadruplex-hairpin-duplex switch.
Doluca, O. and Kaplan, O.I. and Berber, B. and Hekim, N.
bioRxiv
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24 November 2015
A spectral analysis approach to detect actively translated open reading frames in high-resolution ribosome profiling data.
Calviello, L. and Mukherjee, N. and Wyler, E. and Zauber, H. and Hirsekorn, A. and Selbach, M. and Landthaler, M. and Obermayer, B. and Ohler, U.
bioRxiv
: 031625.
13 November 2015
destiny – diffusion maps for large-scale single-cell data in R.
Angerer, P. and Haghverdi, L. and Büttner, M. and Theis, F.J. and Marr, C. and Buettner, F.
bioRxiv
: 023309.
9 October 2015
Genomic DNA transposition induced by human PGBD5.
Henssen, A. and Henaff, E. and Jiang, E. and Eisenberg, A.R. and Carson, J.R. and Villasante, C. and Ray, M. and Still, E. and Burns, M. and Gandara, J. and Feschotte, C. and Mason, C.E. and Kentsis, A.
bioRxiv
: 023887.
3 August 2015
Comprehensive identification and characterization of conserved small ORFs in animals.
Mackowiak, S.D. and Zauber, H. and Bielow, C. and Thiel, D. and Kutz, K. and Calviello, L. and Mastrobuoni, G. and Rajewsky, N. and Kempa, S. and Selbach, M. and Obermayer, B.
bioRxiv
: 017772.
9 April 2015
Changes in postural syntax characterize sensory modulation and natural variation of C. elegans locomotion.
Schwarz, R.F. and Branicky, R. and Grundy, L.J. and Schafer, W.R. and Brown, A.E.X.
bioRxiv
: 017707.
8 April 2015
2014
LIMIX: genetic analysis of multiple traits.
Lippert, C. and Casale, F.P. and Rakitsch, B. and Stegle, O.
bioRxiv
: 003905.
22 May 2014
This list was generated on Fri Apr 26 02:36:08 2024 CEST.
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