Publications

2017

Cheng, J., Avsec, Z., and Gagneur, J. (2017). Sequence features explain most of the mRNA stability variation across genes in yeast. bioRxiv.

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Agerschou, E.D., Mast, C.B., Braun, D. (2017). Emergence of life from trapped nucleotides? Non-equilibrium behavior of oligonucleotides in thermal gradients. Synlett 28, 56-63.

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Fröhlich, F., Kaltenbacher, B, Theis, F.J., Hasenauer, J. (2017). Scalable parameter estimation for genome-scale biochemical reaction networks. Plos Comput Biol 13(1): e1005331.

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Gerland, T.A., Sun, B., Smialowski, P., Lukacs, A., Thomae, A.W., and Imhof, A. (2017). The Drosophila speciation factor HMR localizes to genomic insulator sites. PloS one 12, e0171798.

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Greiss, F., Kriegel, F., Braun, D. (2017). Probing the cooperativity of binding networks with high-throughput thermophoresis. Analytical Chemistry 89 (4), 2592-2597.

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Hinzpeter, F., Gerland, U., Tostevin, F. (2017). Optimal compartmentalization strategies for metabolic microcompartments. Biophys J 112, 767 – 779

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Michel, M., Demel, C., Zacher, B., Schwalb, B., Krebs, S., Blum, H., Gagneur, J., and Cramer, P. (2017). TT-seq captures enhancer landscapes immediately after T-cell stimulation. Mol Syst Biol 13, 920.

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Ponce, L.P., Fenn, N.C., Moritz, N., Krupka, C., Kozik, J.H., Lauber, K., Subklewe, M., and Hopfner, K.P. (2017). SIRPalpha-antibody fusion proteins stimulate phagocytosis and promote elimination of acute myeloid leukemia cells. Oncotarget 8, 11284-11301.

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Collado, J., and Fernandez-Busnadiego, R. (2017). Deciphering the molecular architecture of membrane contact sites by cryo-electron tomography. Biochimica et biophysica acta.

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Schauer, T., Ghavi-Helm, Y., Sexton, T., Albig, C., Regnard, C., Cavalli, G., Furlong, E.E.M., and Becker, P.B. (2017). The Drosophila Dosage Compensation Complex activates target genes by chromosome looping within the active compartment. bioRxiv.

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Barthels, C., Ogrinc, A., Steyer, V., Meier, S., Simon, F., Wimmer, M., Blutke, A., Straub, T., Zimber-Strobl, U., Lutgens, E., et al. (2017). CD40-signalling abrogates induction of RORγt(+) Treg cells by intestinal CD103(+) DCs and causes fatal colitis. Nature Communications 8, 14715.

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Schueder, F., Strauss, M.T., Hoerl, D., Schnitzbauer, J., Schlichthaerle, T., Strauss, S., Yin, P., Harz, H., Leonhardt, H., and Jungmann, R. (2017). Universelles Superauflösungs-Multiplexing durch DNA-Austausch. Angewandte Chemie 129, 4111-4114.

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von Bronk, B., Schaffer, S.A., Gotz, A., and Opitz, M. (2017). Effects of stochasticity and division of labor in toxin production on two-strain bacterial competition in Escherichia coli. PLoS biology 15, e2001457.

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Schnitzbauer, J., Strauss, M.T., Schlichthaerle, T., Schueder, F., and Jungmann, R. (2017). Super-resolution microscopy with DNA-PAINT. Nature protocols 12, 1198-1228.

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Shetty, A., Kallgren, S.P., Demel, C., Maier, K.C., Spatt, D., Alver, B.H., Cramer, P., Park, P.J., and Winston, F. (2017). Spt5 Plays Vital Roles in the Control of Sense and Antisense Transcription Elongation. Molecular cell 66, 77-88 e75.

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Su, T., Cheng, J., Sohmen, D., Hedman, R., Berninghausen, O., von Heijne, G., Wilson, D.N., and Beckmann, R. (2017). The force-sensing peptide VemP employs extreme compaction and secondary structure formation to induce ribosomal stalling. eLife 6.

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Krzyszton, R., Salem, B., Lee, D.J., Schwake, G., Wagner, E., Rädler, J.O. (2017). Microfluidic self-assembly of folate-targeted monomolecular siRNA-lipid nanoparticles. Nanoscale 9, 7442-7453.

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2016

Denk, J., Huber, L., Reithmann, E., and Frey, E. (2016). Active Curved Polymers Form Vortex Patterns on Membranes. Phys Rev Lett 116.

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Dau, T., Edeleva, E.V., Seidel, S.A.I., Stockley, R.A., Braun, D., and Jenne, D.E. (2016). Quantitative analysis of protease recognition by inhibitors in plasma using microscale thermophoresis. Sci Rep-Uk 6, 35413.

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Chatzopoulou, E.I., Roskopf, C.C., Sekhavati, F., Braciak, T.A., Fenn, N.C., Hopfner, K.-P., Oduncu, F.S., Fey, G.H., and Rädler, J.O. (2016). Chip-based platform for dynamic analysis of NK cell cytolysis mediated by a triplebody. Analyst 141, 2284-2295.

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Chlis, N.K., Wolf, F.A., and Theis, F.J. (2016). Model-based branching point detection in single-cell data by K-Branches clustering. bioRxiv.

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Eser, P., Wachutka, L., Maier, K.C., Demel, C., Boroni, M., Iyer, S., Cramer, P., and Gagneur, J. (2016). Determinants of RNA metabolism in the Schizosaccharomyces pombe genome. Mol Syst Biol 12, 857.

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Fröhlich, F., Theis, F.J., Rädler, J.O., and Hasenauer, J. (2016). Parameter estimation for dynamical systems with discrete events and logical operations. Bioinformatics.

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Fröhlich, F., Thomas, P., Kazeroonian, A., Theis, F.J., Grima, R., and Hasenauer, J. (2016). Inference for Stochastic Chemical Kinetics Using Moment Equations and System Size Expansion. Plos Comput Biol 12.

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Greiss, F., Deligiannaki, M., Jung, C., Gaul, U., and Braun, D. (2016). Single-Molecule Imaging in Living Drosophila Embryos with Reflected Light-Sheet Microscopy. Biophys J 110, 939-946.

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Haghverdi, L., Büttner, M., Wolf, F.A., Buettner, F., and Theis, F.J. (2016). Diffusion pseudotime robustly reconstructs lineage branching. Nature methods 13, 845-848.

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Kazeroonian, A., Fröhlich, F., Raue, A., Theis, F.J., and Hasenauer, J. (2016). CERENA: ChEmical REaction Network Analyzer-A Toolbox for the Simulation and Analysis of Stochastic Chemical Kinetics. PloS one 11, e0146732.

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Khmelinskaia, A., Franquelim, H.G., Petrov, E.P., and Schwille, P. (2016). Effect of anchor positioning on binding and diffusion of elongated 3D DNA nanostructures on lipid membranes. J Phys D Appl Phys 49.

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Kretschmer, S., and Schwille, P. (2016). Pattern formation on membranes and its role in bacterial cell division. Current opinion in cell biology 38, 52-59.

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Mura, F., Zaccone., A. (2016). Effects of shear flow on phase nucleation and crystallization. Physical Review E 93, 042803.

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Ramirez, D., Garcia-Soriano, D.A., Raso, A., Feingold, M., Rivas, G., and Schwille, P. (2016). Chiral vortex dynamics on membranes is an intrinsic property of FtsZ, driven by GTP hydrolysis. bioRxiv.

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Schmidt, C., Becker, T., Heuer, A., Braunger, K., Shanmuganathan, V., Pech, M., Berninghausen, O., Wilson, D.N., and Beckmann, R. (2016). Structure of the hypusinylated eukaryotic translation factor eIF-5A bound to the ribosome. Nucleic acids research 44, 1944-1951.

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Schmidt, C., Kowalinski, E., Shanmuganathan, V., Defenouillere, Q., Braunger, K., Heuer, A., Pech, M., Namane, A., Berninghausen, O., Fromont-Racine, M., Jacquier, A., Conti, E., Becker, T., Beckmann, R. (2016). The cryo-EM structure of a ribosome-Ski2-Ski3-Ski8 helicase complex. Science 354, 1431-1433.

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Schwalb, B., Michel, M., Zacher, B., Fruhauf, K., Demel, C., Tresch, A., Gagneur, J., and Cramer, P. (2016). TT-seq maps the human transient transcriptome. Science 352, 1225-1228.

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Vogel, S.K., Greiss, F., Khmelinskaia, A., and Schwille, P. (2016). Control of Lipid Domain Organization by a Biomimetic Contractile Actomyosin Cortex. bioRxiv.

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Eraslan, G., Arloth, J., Martins, J., Iurato, S., Czamara, D., Binder, E.B., Theis, F.J., and Mueller, N.S. (2016). DeepWAS: Directly integrating regulatory information into GWAS using deep learning supports master regulator MEF2C as risk factor for major depressive disorder. bioRxiv.

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Schlichthaerle, T., Strauss, M.T., Schueder, F., Woehrstein, J.B., and Jungmann, R. (2016). DNA nanotechnology and fluorescence applications. Current opinion in biotechnology 39, 41-47.

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2015

Angerer, P., Haghverdi, L., Büttner, M., Theis, F.J., Marr, C., and Buettner, F. (2015). destiny: diffusion maps for large-scale single-cell data in R. Bioinformatics.

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Bader, D.M., Wilkening, S., Lin, G., Tekkedil, M.M., Dietrich, K., Steinmetz, L.M., and Gagneur, J. (2015). Negative feedback buffers effects of regulatory variants. Molecular systems biology 11, 785.

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Haack, T.B., Staufner, C., Kopke, M.G., Straub, B.K., Kolker, S., Thiel, C., Freisinger, P., Baric, I., McKiernan, P.J., Dikow, N., Harting, I., Beisse, F., Burgard, P., Kotzaeridou, U., Kühr, J., Himbert, U., Taylor, R.W., Distelmaier, F., Vockley, J., Ghaloul-Gonzalez, L., Zschocke, J., Kremer, L.S., Graf, E., Schwarzmayr, T., Bader, D.M., Gagneur, J., et al. (2015). Biallelic Mutations in NBAS Cause Recurrent Acute Liver Failure with Onset in Infancy. American journal of human genetics 97, 163-169.

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Reichl, M., Herzog, M., Greiss, F., Wolff, M., and Braun, D. (2015). Understanding the similarity in thermophoresis between single- and double-stranded DNA or RNA. Physical review E, Statistical, nonlinear, and soft matter physics 91, 062709.

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Kretschmer, S., and Schwille, P. (2015). Rekonstitution biologischer Selbstorganisation in vitro. BIOspektrum 21, 148-150.

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Arloth, J., Bader, D.M., Röh, S., and Altmann, A. (2015). Re-Annotator: Annotation Pipeline for Microarray Probe Sequences. PloS one 10, e0139516.

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2014

Fröhlich, F., Hross, S., Theis, F.J., and Hasenauer, J. (2014). Radial Basis Function Approximations of Bayesian Parameter Posterior Densities for Uncertainty Analysis. In: Mendes P., Dada J.O., Smallbone K. (eds) Computational Methods in Systems Biology. CMSB 2014. Lecture Notes in Computer Science, vol 8859. Springer, Cham

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Fröhlich, F., Theis, F.J., and Hasenauer, J. (2014).  Uncertainty Analysis for Non-identifiable Dynamical Systems: Profile Likelihoods, Bootstrapping and More. In: Mendes P., Dada J.O., Smallbone K. (eds) Computational Methods in Systems Biology. CMSB 2014. Lecture Notes in Computer Science, vol 8859. Springer, Cham

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Graf, A., Krebs, S., Heininen-Brown, M., Zakhartchenko, V., Blum, H., and Wolf, E. (2014). Genome activation in bovine embryos: review of the literature and new insights from RNA sequencing experiments. Animal reproduction science 149, 46-58.

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Kretschmer, S., and Schwille, P. (2014). Toward Spatially Regulated Division of Protocells: Insights into the E. coli Min System from in Vitro Studies. Life 4, 915-928.

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Hopfner, K.P. (2014). RIG-I holds the CARDs in a game of self versus nonself. Molecular cell 55, 505-507.

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