GSC 1006: Graduate School of Quantitative Biosciences Munich (QBM)
Final Report Abstract
The molecular biosciences are undergoing a major paradigm shift – away from analyzing individual genes and proteins to studying large molecular machines and cellular pathways, with the ultimate goal of understanding biological systems in their entirety. The emerging study of biomolecular systems faces major methodological and conceptual challenges due to the need for quantitative approaches for the study and characterization of biological systems. This includes the development of sensitive quantitative assays, both for cell-based high throughput and for in vivo analyses; improved measurement techniques that ideally push resolution limits to the single molecule level; statistical methods capable of managing high-dimensional, often noisy, data sets; and mathematical modeling approaches that reduce the dimensionality of parameter spaces and produce mechanistically realistic, experimentally testable predictions. As a result, systemsoriented biological research is inherently an interdisciplinary undertaking, involving biochemistry/structural biology, molecular and organismal genetics, molecular biology, biophysics, biostatistics, bioinformatics, and theoretical physics. The mission of the Graduate School of Quantitative Biosciences Munich (QBM) is to provide a new generation of scientists with the skills and resources to excel in this new multi-disciplinary environment. The school offers a structured PhD program consisting of three components: an interdisciplinary research project, a program of formal lectures and course work including an interdisciplinary core course that covers key problems in bioscience from multiple perspectives, and activities to enhance students’ communication skills. Beyond its educational mission, the school provides a framework for interdisciplinary collaboration between the participating PIs and groups, thereby directly advancing the aims of quantitative, systems-oriented bioscience. The school was built on LMU Munich’s strengths in biochemistry and physics, complemented by adjacent disciplines, in particular applied mathematics and medicine, and by neighboring institutions (MPI Biochemistry, Helmholtz Center Munich). Encompassing a wide range of methodological approaches, the school concentrates thematically on the control of gene expression in all its aspects and the interplay of different control mechanisms in regulatory networks, a fundamental problem that is well suited for the envisioned quantitative and systemic analysis and has important medical implications. With its strong emphasis on anchoring theoretical analysis in advanced quantitative experimentation, its focus on the control of gene expression, and the excellence of the participating scientists, the school as of today has a unique position within the European scientific landscape.
Link to the final report
https://doi.org/10.2314/KXP:1702177580
Publications
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(2013). Transcriptome surveillance by selective termination of noncoding RNA synthesis. Cell 155, 1075-1087
Schulz, Daniel; Schwalb, Bjoern; Kiesel, Anja; Baejen, Carlo; Torkler, Phillipp; Gagneur, Julien; Soeding, Johannes & Cramer, Patrick
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(2014). ATP puts the brake on DNA double‐strand break repair. Bioessays 36, 1170-1178
Hopfner, Karl‐Peter
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(2014). Genome activation in bovine embryos: review of the literature and new insights from RNA sequencing experiments. Animal reproduction science 149, 46-58
Graf, Alexander; Krebs, Stefan; Heininen-Brown, Mari; Zakhartchenko, Valeri; Blum, Helmut & Wolf, Eckhard
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(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
Fröhlich, Fabian; Hross, Sabrina; Theis, Fabian J. & Hasenauer, Jan
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(2014). RIG-I holds the CARDs in a game of self versus nonself. Molecular cell 55, 505-507
Hopfner, Karl-Peter
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(2014). Toward Spatially Regulated Division of Protocells: Insights into the E. coli Min System from in Vitro Studies. Life 4, 915-928
Kretschmer, Simon & Schwille, Petra
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(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
Fröhlich, Fabian; Theis, Fabian J. & Hasenauer, Jan
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(2015). Biallelic Mutations in NBAS Cause Recurrent Acute Liver Failure with Onset in Infancy. American journal of human genetics 97, 163-169
Haack, Tobias B.; Staufner, Christian; Köpke, Marlies G.; Straub, Beate K.; Kölker, Stefan; Thiel, Christian; Freisinger, Peter; Baric, Ivo; McKiernan, Patrick J.; Dikow, Nicola; Harting, Inga; Beisse, Flemming; Burgard, Peter; Kotzaeridou, Urania; Kühr, Joachim; Himbert, Urban; Taylor, Robert W.; Distelmaier, Felix; Vockley, Jerry; ... & Prokisch, Holger
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(2015). destiny: diffusion maps for large-scale single-cell data in R. Bioinformatics
Angerer, Philipp; Haghverdi, Laleh; Büttner, Maren; Theis, Fabian J.; Marr, Carsten & Buettner, Florian
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(2015). Marker-free detection of progenitor cell differentiation by analysis of Brownian motion in microwells. Integrative Biology 7, 178-183
Sekhavati, Farzad; Endele, Max; Rappl, Susanne; Marel, Anna-Kristina; Schroeder, Timm & Rädler, Joachim O.
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(2015). Negative feedback buffers effects of regulatory variants. Molecular systems biology 11, 785
Bader, Daniel M; Wilkening, Stefan; Lin, Gen; Tekkedil, Manu M; Dietrich, Kim; Steinmetz, Lars M & Gagneur, Julien
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(2015). Re-Annotator: Annotation Pipeline for Microarray Probe Sequences. PloS one 10, e0139516
Arloth, Janine; Bader, Daniel M.; Röh, Simone & Altmann, Andre
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(2015). Rekonstitution biologischer Selbstorganisation in vitro. BIOspektrum 21, 148-150
Kretschmer, Simon & Schwille, Petra
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(2015). Structure of a human translation termination complex. Nucleic acids research 43, 8615-8626
Matheisl, Sarah; Berninghausen, Otto; Becker, Thomas & Beckmann, Roland
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(2015). Translational arrest by a prokaryotic signal recognition particle is mediated by RNA interactions. Nature structural & molecular biology 22, 767-773
Beckert, Bertrand; Kedrov, Alexej; Sohmen, Daniel; Kempf, Georg; Wild, Klemens; Sinning, Irmgard; Stahlberg, Henning; Wilson, Daniel N & Beckmann, Roland
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(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
Reichl, Maren; Herzog, Mario; Greiss, Ferdinand; Wolff, Manuel & Braun, Dieter
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(2016). Structure of the hypusinylated eukaryotic translation factor eIF-5A bound to the ribosome. Nucleic acids research 44, 1944- 1951
Schmidt, Christian; Becker, Thomas; Heuer, André; Braunger, Katharina; Shanmuganathan, Vivekanandan; Pech, Markus; Berninghausen, Otto; Wilson, Daniel N. & Beckmann, Roland
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(2016). Active Curved Polymers Form Vortex Patterns on Membranes. Phys Rev Lett 116
Denk, Jonas; Huber, Lorenz; Reithmann, Emanuel & Frey, Erwin
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(2016). CERENA: ChEmical REaction Network Analyzer-A Toolbox for the Simulation and Analysis of Stochastic Chemical Kinetics. PloS one 11, e0146732
Kazeroonian, Atefeh; Fröhlich, Fabian; Raue, Andreas; Theis, Fabian J. & Hasenauer, Jan
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(2016). Chip-based platform for dynamic analysis of NK cell cytolysis mediated by a triplebody. Analyst 141, 2284-2295
Chatzopoulou, Elisavet I.; Roskopf, Claudia C.; Sekhavati, Farzad; Braciak, Todd A.; Fenn, Nadja C.; Hopfner, Karl-Peter; Oduncu, Fuat S.; Fey, Georg H. & Rädler, Joachim O.
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(2016). Chiral vortex dynamics on membranes is an intrinsic property of FtsZ, driven by GTP hydrolysis. bioRxiv
Ramirez, Diego; García-Soriano, Daniela A.; Raso, Ana; Feingold, Mario; Rivas, Germán & Schwille, Petra
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(2016). DeepWAS: Directly integrating regulatory information into GWAS using deep learning supports master regulator MEF2C as risk factor for major depressive disorder. bioRxiv
Arloth, Janine; Eraslan, Gökcen; Andlauer, Till F.M.; Martins, Jade; Iurato, Stella; Kühnel, Brigitte; Waldenberger, Melanie; Frank, Josef; Gold, Ralf; Hemmer, Bernhard; Luessi, Felix; Nischwitz, Sandra; Paul, Friedemann; Wiendl, Heinz; Gieger, Christian; Heilmann-Heimbach, Stefanie; Kacprowski, Tim; Laudes, Matthias; Meitinger, Thomas; ... & Mueller, Nikola S.
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(2016). Determinants of RNA metabolism in the Schizosaccharomyces pombe genome. Mol Syst Biol 12, 857
Eser, Philipp; Wachutka, Leonhard; Maier, Kerstin C; Demel, Carina; Boroni, Mariana; Iyer, Srignanakshi; Cramer, Patrick & Gagneur, Julien
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(2016). Diffusion pseudotime robustly reconstructs lineage branching. Nature methods 13, 845-848
Haghverdi, Laleh; Büttner, Maren; Wolf, F. Alexander; Buettner, Florian & Theis, Fabian J.
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(2016). DNA nanotechnology and fluorescence applications. Current opinion in biotechnology 39, 41- 47
Schlichthaerle, Thomas; Strauss, Maximilian T; Schueder, Florian; Woehrstein, Johannes B & Jungmann, Ralf
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(2016). Dual-targeting triplebody 33-3-19 mediates selective lysis of biphenotypic CD19+ CD33+ leukemia cells. Oncotarget 7, 22579
Roskopf, Claudia C.; Braciak, Todd A.; Fenn, Nadja C.; Kobold, Sebastian; Fey, Georg H.; Hopfner, Karl-Peter & Oduncu, Fuat S.
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(2016). Effect of anchor positioning on binding and diffusion of elongated 3D DNA nanostructures on lipid membranes. J Phys D Appl Phys 49
Khmelinskaia, Alena; Franquelim, Henri G; Petrov, Eugene P & Schwille, Petra
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(2016). Effects of shear flow on phase nucleation and crystallization. Physical Review E 93, 042803
Mura, Federica & Zaccone, Alessio
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(2016). Inference for Stochastic Chemical Kinetics Using Moment Equations and System Size Expansion. Plos Comput Biol 12
Fröhlich, Fabian; Thomas, Philipp; Kazeroonian, Atefeh; Theis, Fabian J.; Grima, Ramon & Hasenauer, Jan
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(2016). Parameter estimation for dynamical systems with discrete events and logical operations. Bioinformatics
Fröhlich, Fabian; Theis, Fabian J; Rädler, Joachim O & Hasenauer, Jan
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(2016). Pattern formation on membranes and its role in bacterial cell division. Current opinion in cell biology 38, 52-59
Kretschmer, Simon & Schwille, Petra
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(2016). Quantitative analysis of protease recognition by inhibitors in plasma using microscale thermophoresis. Sci Rep-Uk 6, 35413
Dau, T.; Edeleva, E. V.; Seidel, S. A. I.; Stockley, R. A.; Braun, D. & Jenne, D. E.
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(2016). Single-Molecule Imaging in Living Drosophila Embryos with Reflected Light-Sheet Microscopy. Biophys J 110, 939-946
Greiss, Ferdinand; Deligiannaki, Myrto; Jung, Christophe; Gaul, Ulrike & Braun, Dieter
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(2016). The cryo-EM structure of a ribosome-Ski2-Ski3-Ski8 helicase complex. Science 354, 1431-1433
Schmidt, Christian; Kowalinski, Eva; Shanmuganathan, Vivekanandan; Defenouillère, Quentin; Braunger, Katharina; Heuer, André; Pech, Markus; Namane, Abdelkader; Berninghausen, Otto; Fromont-Racine, Micheline; Jacquier, Alain; Conti, Elena; Becker, Thomas & Beckmann, Roland
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(2016). TT-seq maps the human transient transcriptome. Science 352, 1225-1228
Schwalb, Björn; Michel, Margaux; Zacher, Benedikt; Frühauf, Katja; Demel, Carina; Tresch, Achim; Gagneur, Julien & Cramer, Patrick
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(2017). Emergence of life from trapped nucleotides? Non-equilibrium behavior of oligonucleotides in thermal gradients. Synlett 28, 56-63
Mast, Christof; Braun, Dieter & Agerschou, Emil
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(2017). CD40-signalling abrogates induction of RORγt(+) Treg cells by intestinal CD103(+) DCs and causes fatal colitis. Nature Communications 8, 14715
Barthels, Christian; Ogrinc, Ana; Steyer, Verena; Meier, Stefanie; Simon, Ferdinand; Wimmer, Maria; Blutke, Andreas; Straub, Tobias; Zimber-Strobl, Ursula; Lutgens, Esther; Marconi, Peggy; Ohnmacht, Caspar; Garzetti, Debora; Stecher, Bärbel & Brocker, Thomas
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(2017). Chromosome topology guides the Drosophila Dosage Compensation Complex for target gene activation. EMBO reports 18, 1854-1868
Schauer, Tamás; Ghavi‐helm, Yad; Sexton, Tom; Albig, Christian; Regnard, Catherine; Cavalli, Giacomo; Furlong, Eileen Em & Becker, Peter B.
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(2017). Cis-regulatory elements explain most of the mRNA stability variation across genes in yeast. Rna 23, 1648-1659
Cheng, Jun; Maier, Kerstin C.; Avsec, Žiga; Rus, Petra & Gagneur, Julien
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(2017). compleXView: a server for the interpretation of protein abundance and connectivity information to identify protein complexes. Nucleic acids research
Solis-Mezarino, Victor & Herzog, Franz
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(2017). Control of lipid domain organization by a biomimetic contractile actomyosin cortex. eLife 6
Vogel, Sven Kenjiro; Greiss, Ferdinand; Khmelinskaia, Alena & Schwille, Petra
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(2017). Deciphering the molecular architecture of membrane contact sites by cryo-electron tomography. Biochimica et biophysica acta
Collado, Javier & Fernández-Busnadiego, Rubén
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(2017). Effects of stochasticity and division of labor in toxin production on two-strain bacterial competition in Escherichia coli. PLoS biology 15, e2001457
von Bronk, Benedikt; Schaffer, Sophia Anna; Götz, Alexandra & Opitz, Madeleine
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(2017). Efficient parameterization of large-scale mechanistic models enables drug response prediction for cancer cell lines. bioRxiv, 174094
Fröhlich, Fabian; Kessler, Thomas; Weindl, Daniel; Shadrin, Alexey; Schmiester, Leonard; Hache, Hendrik; Muradyan, Artur; Schütte, Moritz; Lim, Ji-Hyun; Heinig, Matthias; Theis, Fabian J.; Lehrach, Hans; Wierling, Christoph; Lange, Bodo & Hasenauer, Jan
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(2017). Exploiting ecology in drug pulse sequences in favour of population reduction. Plos Comput Biol 13, e1005747
Bauer, Marianne; Graf, Isabella R.; Ngampruetikorn, Vudtiwat; Stephens, Greg J. & Frey, Erwin
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(2017). Fast, background-free DNA-PAINT imaging using FRET-based probes. Nano letters 17, 6428-6434
Auer, Alexander; Strauss, Maximilian T.; Schlichthaerle, Thomas & Jungmann, Ralf
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(2017). Generic transport mechanisms for molecular traffic in cellular protrusions. Phys Rev Lett 118, 128101
Graf, Isabella R. & Frey, Erwin
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(2017). Genetic diagnosis of Mendelian disorders via RNA sequencing. Nat Commun 8, 15824
Kremer, Laura S.; Bader, Daniel M.; Mertes, Christian; Kopajtich, Robert; Pichler, Garwin; Iuso, Arcangela; Haack, Tobias B.; Graf, Elisabeth; Schwarzmayr, Thomas; Terrile, Caterina; Koňaříková, Eliška; Repp, Birgit; Kastenmüller, Gabi; Adamski, Jerzy; Lichtner, Peter; Leonhardt, Christoph; Funalot, Benoit; Donati, Alice; Tiranti, Valeria; ... & Prokisch, Holger
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(2017). GenoGAM: genome-wide generalized additive models for ChIP-Seq analysis. Bioinformatics, btx150
Stricker, Georg; Engelhardt, Alexander; Schulz, Daniel; Schmid, Matthias; Tresch, Achim & Gagneur, Julien
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(2017). GenSSI 2.0: Multi-experiment structural identifiability analysis of SBML models. Bioinformatics
Ligon, Thomas S; Fröhlich, Fabian; Chiş, Oana T; Banga, Julio R; Balsa-Canto, Eva & Hasenauer, Jan
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(2017). High-speed AFM reveals the inner workings of the MinDE protein oscillator. Nano letters
Miyagi, Atsushi; Ramm, Beatrice; Schwille, Petra & Scheuring, Simon
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(2017). Identification of a plasma miRNA biomarker signature for allergic asthma: A translational approach. Allergy 72, 1962-1971
Milger, K.; Götschke, J.; Krause, L.; Nathan, P.; Alessandrini, F.; Tufman, A.; Fischer, R.; Bartel, S.; Theis, F. J.; Behr, J.; Dehmel, S.; Mueller, N. S.; Kneidinger, N. & Krauss‐Etschmann, S.
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(2017). In Situ Architecture and Cellular Interactions of PolyQ Inclusions. Cell 171, 179-187 e110
Bäuerlein, Felix J.B.; Saha, Itika; Mishra, Archana; Kalemanov, Maria; Martínez-Sánchez, Antonio; Klein, Rüdiger; Dudanova, Irina; Hipp, Mark S.; Hartl, F. Ulrich; Baumeister, Wolfgang & Fernández-Busnadiego, Rubén
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(2017). Large-scale modulation of reconstituted Min protein patterns and gradients by defined mutations in MinE’s membrane targeting sequence. PloS one 12, e0179582
Kretschmer, Simon; Zieske, Katja & Schwille, Petra
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(2017). Matrix composition determines the dimensions of Bacillus subtilis NCIB 3610 biofilm colonies grown on LB agar. RSC Advances 7, 31886-31898
Kesel, Sara; von Bronk, Benedikt; Falcón García, Carolina; Götz, Alexandra; Lieleg, Oliver & Opitz, Madeleine
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(2017). Mechanistic hierarchical population model identifies latent causes of cell-to-cell variability. bioRxiv, 171561
Loos, Carolin; Moeller, Katharina; Fröhlich, Fabian; Hucho, Tim & Hasenauer, Jan
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(2017). Microfluidic self-assembly of folate-targeted monomolecular siRNA-lipid nanoparticles. Nanoscale 9, 7442- 7453
Krzysztoń, R.; Salem, B.; Lee, D. J.; Schwake, G.; Wagner, E. & Rädler, J. O.
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(2017). Model-based branching point detection in single-cell data by K-Branches clustering. Bioinformatics
Chlis, Nikolaos K.; Wolf, F. Alexander & Theis, Fabian J.
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(2017). Modeling positional effects of regulatory sequences with spline transformations increases prediction accuracy of deep neural networks. Bioinformatics
Avsec, Žiga; Barekatain, Mohammadamin; Cheng, Jun & Gagneur, Julien
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(2017). Optimal compartmentalization strategies for metabolic microcompartments. Biophys J 112, 767 – 779
Hinzpeter, Florian; Gerland, Ulrich & Tostevin, Filipe
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(2017). Organs on chip approach: a tool to evaluate cancer-immune cells interactions. Sci Rep-Uk 7, 12737
Biselli, Elena; Agliari, Elena; Barra, Adriano; Bertani, Francesca Romana; Gerardino, Annamaria; De Ninno, Adele; Mencattini, Arianna; Di Giuseppe, Davide; Mattei, Fabrizio; Schiavoni, Giovanna; Lucarini, Valeria; Vacchelli, Erika; Kroemer, Guido; Di Natale, Corrado; Martinelli, Eugenio & Businaro, Luca
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(2017). PESTO: Parameter EStimation TOolbox. Bioinformatics
Stapor, Paul; Weindl, Daniel; Ballnus, Benjamin; Hug, Sabine; Loos, Carolin; Fiedler, Anna; Krause, Sabrina; Hroß, Sabrina; Fröhlich, Fabian & Hasenauer, Jan
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(2017). Probing the cooperativity of binding networks with high-throughput thermophoresis. Analytical Chemistry 89 (4), 2592-2597
Greiss, Ferdinand; Kriegel, Franziska & Braun, Dieter
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(2017). Scalable parameter estimation for genome-scale biochemical reaction networks. Plos Comput Biol 13(1): e1005331
Fröhlich, Fabian; Kaltenbacher, Barbara; Theis, Fabian J. & Hasenauer, Jan
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(2017). Sen1 has unique structural features grafted on the architecture of the Upf1-like helicase family. The EMBO journal 36, 1590-1604
Leonaitė, Bronislava; Han, Zhong; Basquin, Jérôme; Bonneau, Fabien; Libri, Domenico; Porrua, Odil & Conti, Elena
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(2017). Single cells make big data: New challenges and opportunities in transcriptomics. Current Opinion in Systems Biology 4, 85-91
Angerer, Philipp; Simon, Lukas; Tritschler, Sophie; Wolf, F. Alexander; Fischer, David & Theis, Fabian J.
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(2017). SIRPalpha-antibody fusion proteins stimulate phagocytosis and promote elimination of acute myeloid leukemia cells. Oncotarget 8, 11284-11301
Ponce, Laia Pascual; Fenn, Nadja C.; Moritz, Nadine; Krupka, Christina; Kozik, Jan-Hendrik; Lauber, Kirsten; Subklewe, Marion & Hopfner, Karl-Peter
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(2017). Spt5 Plays Vital Roles in the Control of Sense and Antisense Transcription Elongation. Molecular cell 66, 77-88 e75
Shetty, Ameet; Kallgren, Scott P.; Demel, Carina; Maier, Kerstin C.; Spatt, Dan; Alver, Burak H.; Cramer, Patrick; Park, Peter J. & Winston, Fred
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(2017). Super-resolution microscopy with DNA-PAINT. Nature protocols 12, 1198-1228
Schnitzbauer, Joerg; Strauss, Maximilian T; Schlichthaerle, Thomas; Schueder, Florian & Jungmann, Ralf
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(2017). Systematic single-cell analysis provides new insights into heterogeneity and plasticity of the pancreas. Molecular metabolism 6, 974-990
Tritschler, Sophie; Theis, Fabian J.; Lickert, Heiko & Böttcher, Anika
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(2017). The Drosophila Dosage Compensation Complex activates target genes by chromosome looping within the active compartment. bioRxiv.
Schauer, Tamás; Ghavi-Helm, Yad; Sexton, Tom; Albig, Christian; Regnard, Catherine; Cavalli, Giacomo; Furlong, Eileen E. M. & Becker, Peter B.
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(2017). The Drosophila speciation factor HMR localizes to genomic insulator sites. PloS one 12, e0171798
Gerland, Thomas Andreas; Sun, Bo; Smialowski, Pawel; Lukacs, Andrea; Thomae, Andreas Walter & Imhof, Axel
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(2017). The force-sensing peptide VemP employs extreme compaction and secondary structure formation to induce ribosomal stalling. eLife 6
Su, Ting; Cheng, Jingdong; Sohmen, Daniel; Hedman, Rickard; Berninghausen, Otto; von Heijne, Gunnar; Wilson, Daniel N & Beckmann, Roland
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(2017). The Munich MIDY Pig Biobank – A unique resource for studying organ crosstalk in diabetes. Mol Metab 6, 931-940
Blutke, Andreas; Renner, Simone; Flenkenthaler, Florian; Backman, Mattias; Haesner, Serena; Kemter, Elisabeth; Ländström, Erik; Braun-Reichhart, Christina; Albl, Barbara; Streckel, Elisabeth; Rathkolb, Birgit; Prehn, Cornelia; Palladini, Alessandra; Grzybek, Michal; Krebs, Stefan; Bauersachs, Stefan; Bähr, Andrea; Brühschwein, Andreas; Deeg, Cornelia A.; ... & Wolf, Eckhard
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(2017). The PomXYZ Proteins Self-Organize on the Bacterial Nucleoid to Stimulate Cell Division. Developmental Cell 41, 299-314. e213
Schumacher, Dominik; Bergeler, Silke; Harms, Andrea; Vonck, Janet; Huneke-Vogt, Sabrina; Frey, Erwin & Søgaard-Andersen, Lotte
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(2017). TT-seq captures enhancer landscapes immediately after T-cell stimulation. Mol Syst Biol 13, 920
Michel, Margaux; Demel, Carina; Zacher, Benedikt; Schwalb, Björn; Krebs, Stefan; Blum, Helmut; Gagneur, Julien & Cramer, Patrick
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(2017). Universelles Superauflösungs- Multiplexing durch DNA-Austausch. Angewandte Chemie 129, 4111-4114
Schueder, Florian; Strauss, Maximilian T.; Hoerl, David; Schnitzbauer, Joerg; Schlichthaerle, Thomas; Strauss, Sebastian; Yin, Peng; Harz, Hartmann; Leonhardt, Heinrich & Jungmann, Ralf
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(2017). Visualizing the Assembly Pathway of Nucleolar Pre-60S Ribosomes. Cell 171, 1599-1610. e1514
Kater, Lukas; Thoms, Matthias; Barrio-Garcia, Clara; Cheng, Jingdong; Ismail, Sherif; Ahmed, Yasar Luqman; Bange, Gert; Kressler, Dieter; Berninghausen, Otto; Sinning, Irmgard; Hurt, Ed & Beckmann, Roland
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(2018). OCR-Stats: Robust estimation and statistical testing of mitochondrial respiration activities using Seahorse XF Analyzer
Yépez, Vicente A.; Kremer, Laura S.; Iuso, Arcangela; Gušić, Mirjana; Kopajtich, Robert; Koňaříková, Eliška; Nadel, Agnieszka; Wachutka, Leonhard; Prokisch, Holger & Gagneur, Julien
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Mutations in MDH2, Encoding a Krebs Cycle Enzyme, Cause Early-Onset Severe Encephalopathy. The American Journal of Human Genetics 100, 151-159
Ait-El-Mkadem, Samira; Dayem-Quere, Manal; Gusic, Mirjana; Chaussenot, Annabelle; Bannwarth, Sylvie; François, Bérengère; Genin, Emmanuelle C.; Fragaki, Konstantina; Volker-Touw, Catharina L.M.; Vasnier, Christelle; Serre, Valérie; van Gassen, Koen L.I.; Lespinasse, Françoise; Richter, Susan; Eisenhofer, Graeme; Rouzier, Cécile; Mochel, Fanny; De Saint-Martin, Anne; Abi Warde, Marie-Thérèse; ... & Paquis-Flucklinger, Véronique
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(2017). Assessment of batchcorrection methods for scRNA-seq data with a new test metric. bioRxiv, 200345
Büttner, Maren; Miao, Zhichao; Wolf, F. Alexander; Teichmann, Sarah A. & Theis, Fabian J.
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(2017). Broken detailed balance and non-equilibrium dynamics in living systems
Gnesotto, F. S.; Mura, F.; Gladrow, J. & Broedersz, C. P.
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(2017). Scalable Inference of Ordinary Differential Equation Models of Biochemical Processes. arXiv preprint arXiv:171108079
Fröhlich, Fabian; Loos, Carolin & Hasenauer, Jan
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(2017). Toll-like receptor 7/8 agonists stimulate plasmacytoid dendritic cells to initiate TH17-deviated acute contact dermatitis in human subjects. Journal of Allergy and Clinical Immunology
Garzorz-Stark, Natalie; Lauffer, Felix; Krause, Linda; Thomas, Jenny; Atenhan, Anne; Franz, Regina; Roenneberg, Sophie; Boehner, Alexander; Jargosch, Manja; Batra, Richa; Mueller, Nikola S.; Haak, Stefan; Groß, Christina; Groß, Olaf; Traidl-Hoffmann, Claudia; Theis, Fabian J.; Schmidt-Weber, Carsten B.; Biedermann, Tilo; Eyerich, Stefanie; ... & Eyerich, Kilian
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(2018), Complex microbial systems across different levels of description, Physical Biology, 15, 5
von Bronk, Benedikt; Götz, Alexandra & Opitz, Madeleine
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(2018). Benchmarking optimization methods for parameter estimation in large kinetic models. bioRxiv
Villaverde, Alejandro F.; Fröhlich, Fabian; Weindl, Daniel; Hasenauer, Jan & Banga, Julio R.
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(2018). Guiding 3D cell migration in deformed synthetic hydrogel microstructures. Soft matter 14, 2816 -2826
Dietrich, Miriam; Le Roy, Hugo; Brückner, David B.; Engelke, Hanna; Zantl, Roman; Rädler, Joachim O. & Broedersz, Chase P.
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(2018). In Vitro Reconstitution of Self-Organizing Protein Patterns on Supported Lipid Bilayers J. Vis. Exp. (137). e58139
Ramm, Beatrice; Glock, Philipp & Schwille, Petra
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(2018). Intricate structure of the interphase chromocenter revealed by the analysis of a factor involved in species formation
Kochanova, Natalia Y.; Schauer, Tamas; Mathias, Grusha Primal; Lukacs, Andrea; Schmidt, Andreas; Flatley, Andrew; Schepers, Aloys; Thomae, Andreas W. & Imhof, Axel
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(2018). Membrane sculpting by curved DNA origami scaffolds. Nat Commun 9, 811
Franquelim, Henri G.; Khmelinskaia, Alena; Sobczak, Jean-Philippe; Dietz, Hendrik & Schwille, Petra
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(2018). MinE conformational switching confers robustness on self-organized Min protein patterns. Proceedings of the National Academy of Sciences of the United States of America
Denk, Jonas; Kretschmer, Simon; Halatek, Jacob; Hartl, Caroline; Schwille, Petra & Frey, Erwin
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(2018). Multi-Experiment Nonlinear Mixed Effect Modeling of Single-Cell Translation Kinetics after Transfection
Fröhlich, Fabian; Reiser, Anita; Fink, Laura; Woschée, Daniel; Ligon, Thomas; Theis, Fabian Joachim; Rädler, Joachim Oskar & Hasenauer, Jan
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(2018). Multi-experiment nonlinear mixed effect modeling of single-cell translation kinetics after transfection. npj Systems Biology and applications 4, Article number: 42
Fröhlich, Fabian; Reiser, Anita; Fink, Laura; Woschée, Daniel; Ligon, Thomas; Theis, Fabian Joachim; Rädler, Joachim Oskar & Hasenauer, Jan
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(2018). Non-equilibrium scaling behaviour in driven soft biological assemblies. arXiv preprint arXiv:180302797
Mura, Federica; Gradziuk, Grzegorz & Broedersz, Chase P.
-
(2018). Optimization and uncertainty analysis of ODE models using second order adjoint sensitivity analysis. bioRxiv
Stapor, Paul; Fröhlich, Fabian & Hasenauer, Jan
-
(2018). Regulation of Pom cluster dynamics in Myxococcus xanthus
Bergeler, Silke & Frey, Erwin
-
(2018). Reverse and forward engineering of protein pattern formation. Philosophical Transactions of the Royal Society B: Biological Sciences 373
Kretschmer, Simon; Harrington, Leon & Schwille, Petra
-
(2018). Self-organized system size oscillation of a stochastic lattice-gas model
Bojer, Mareike; Graf, Isabella R. & Frey, Erwin
-
(2018). Single Cell Microarrays Fabricated by Microscale Plasma-Initiated Protein Patterning (μPIPP). In Cell-Based Microarrays (Springer), pp. 41-54
Reiser, Anita; Zorn, Matthias Lawrence; Murschhauser, Alexandra & Rädler, Joachim Oskar
-
(2018). Single-cell RNA sequencing reveals developmental heterogeneity of blastomeres during major genome activation in bovine embryos. Sci Rep 8, 4071
Lavagi, Ilaria; Krebs, Stefan; Simmet, Kilian; Beck, Andrea; Zakhartchenko, Valeri; Wolf, Eckhard & Blum, Helmut
-
(2018). Single-molecule nucleosome remodeling by INO80 and effects of histone tails. FEBS letters
Schwarz, Marianne; Schall, Kevin; Kallis, Eleni; Eustermann, Sebastian; Guariento, Mara; Moldt, Manuela; Hopfner, Karl‐Peter & Michaelis, Jens
-
(2018). Structural basis for ATP-dependent chromatin remodelling by the INO80 complex. Nature
Eustermann, Sebastian; Schall, Kevin; Kostrewa, Dirk; Lakomek, Kristina; Strauss, Mike; Moldt, Manuela & Hopfner, Karl-Peter
-
(2018). The Folding Pathway of an Ig Domain is Conserved On and Off the Ribosome. bioRxiv
Tian, Pengfei; Steward, Annette; Kudva, Renuka; Su, Ting; Shilling, Patrick J.; Nickson, Adrian A.; Hollins, Jeffrey J.; Beckmann, Roland; von Heijne, Gunnar; Clarke, Jane & Best, Robert B.
-
(2018). The MinDE system is a generic spatial cue for membrane protein distribution in vitro. Nat Commun
Ramm, Beatrice; Glock, Philipp; Mücksch, Jonas; Blumhardt, Philipp; García-Soriano, Daniela A.; Heymann, Michael & Schwille, Petra
-
(2018). Thermophoretic forces on a mesoscopic scale. Soft Matter
Burelbach, Jérôme; Brückner, David B.; Frenkel, Daan & Eiser, Erika
-
A test metric for assessing single-cell RNA-seq batch correction. Nature Methods, 16, 43-49 (2019)
Büttner, Maren; Miao, Zhichao; Wolf, F. Alexander; Teichmann, Sarah A. & Theis, Fabian J.
-
Chromatyping: Reconstructing Nucleosome Profiles from NOMe Sequencing Data; Research in Computational Molecular Biology. RECOMB 2018. Lecture Notes in Computer Science. 2018;10812:60-61
Chakraborty, Shounak; Canzar, Stefan; Marschall, Tobias & Schulz, Marcel H.
-
Control of Membrane Binding and Diffusion of Cholesteryl-Modified DNA Origami Nanostructures by DNA Spacers; Langmuir, 2018, 34, 49, 14921-14931
Khmelinskaia, Alena; Mücksch, Jonas; Petrov, Eugene P.; Franquelim, Henri G. & Schwille, Petra
-
Factor cooperation for chromosome discrimination in Drosophila, Nucleic Acids Res. 2019 Feb 28;47(4):1706-1724
Albig, Christian; Tikhonova, Evgeniya; Krause, Silke; Maksimenko, Oksana; Regnard, Catherine & Becker, Peter B.
-
FCS Analysis of Protein Mobility on Lipid Monolayers, Open Archive Published: March 28, 2018
Khmelinskaia, Alena; Mücksch, Jonas; Conci, Franco; Chwastek, Grzegorz & Schwille, Petra
-
Locality of interactions in three-strain bacterial competition in E. coli; Physical Biology, Volume 16, Number 1
von Bronk, Benedikt; Götz, Alexandra & Opitz, Madeleine
-
Nano letters, 18, 7, 4626-4630
Deußner-Helfmann, Nina S.; Auer, Alexander; Strauss, Maximilian T.; Malkusch, Sebastian; Dietz, Marina S.; Barth, Hans-Dieter; Jungmann, Ralf & Heilemann, Mike
-
Nanometer‐scale Multiplexed Super‐Resolution Imaging with an Economic 3D‐DNA‐PAINT Microscope
Auer, Alexander; Schlichthaerle, Thomas; Woehrstein, Johannes B.; Schueder, Florian; Strauss, Maximilian T.; Grabmayr, Heinrich & Jungmann, Ralf
-
OUTRIDER: A statistical method for detecting aberrantly expressed genes in RNA sequencing data, AJHG, 2018
Brechtmann, Felix; Mertes, Christian; Matusevičiūtė, Agnė; Yépez, Vicente A.; Avsec, Žiga; Herzog, Maximilian; Bader, Daniel M.; Prokisch, Holger & Gagneur, Julien
-
Photo- Induced Depletion of Binding Sites in DNA-PAINT Microscopy; Molecules (2018); 23(12): 3165
Blumhardt, Philipp; Stein, Johannes; Mücksch, Jonas; Stehr, Florian; Bauer, Julian; Jungmann, Ralf & Schwille, Petra
-
Plasmonic Nanosensors Reveal a Height Dependence of MinDE Protein Oscillations on Membrane Features, J. Am. Chem. Soc.2018, 140, 51
Ye, Weixiang; Celiksoy, Sirin; Jakab, Arpad; Khmelinskaia, Alena; Heermann, Tamara; Raso, Ana; Wegner, Seraphine V.; Rivas, Germán; Schwille, Petra; Ahijado-Guzmán, Rubén & Sönnichsen, Carsten
-
Ribosome–NatA architecture reveals that rRNA expansion segments coordinate N-terminal acetylation, Nature Structural & Molecular Biology 26, 35–39 (2019)
Knorr, Alexandra G.; Schmidt, Christian; Tesina, Petr; Berninghausen, Otto; Becker, Thomas; Beatrix, Birgitta & Beckmann, Roland
-
True equilibrium measurement of transcription factor-DNA binding affinities using automated polarization microscopy, Nat Commun. 2018 Apr 23;9(1):1605
Jung, Christophe; Bandilla, Peter; von Reutern, Marc; Schnepf, Max; Rieder, Susanne; Unnerstall, Ulrich & Gaul, Ulrike
-
(2017). Beyond pseudotime: Following T-cell maturation in single-cell RNAseq time series
Fischer, David S.; Fiedler, Anna K.; Kernfeld, Eric M.; Genga, Ryan M. J.; Bastidas-Ponce, Aimée; Bakhti, Mostafa; Lickert, Heiko; Hasenauer, Jan; Maehr, Rene & Theis, Fabian J.
-
(2017). Multireference spectral library yields almost complete coverage of heterogeneous LC-MS/MS data sets. bioRxiv, 180448
Ammar, Constantin; Berchtold, Evi; Csaba, Gergely; Schmidt, Andreas; Imhof, Axel & Zimmer, Ralf
-
(2018). Altered Localization of Hybrid Incompatibility Proteins in Drosophila, Molecular Biology and Evolution, msz105
Cooper, Jacob Carter; Lukacs, Andrea; Reich, Shelley; Schauer, Tamas; Imhof, Axel & Phadnis, Nitin
-
(2018). Modular modeling improves the predictions of genetic variant effects on splicing
Cheng, Jun; Nguyen, Thi Yen Duong; Cygan, Kamil J.; Çelik, Muhammed Hasan; Fairbrother, William G.; Avsec, žiga & Gagneur, Julien
-
(2019) ATAC-seq reveals regional differences in enhancer accessibility during the establishment of spatial coordinates in the Drosophila blastoderm. Genome Research, 29(5): 771-783
Bozek, Marta; Cortini, Roberto; Storti, Andrea Ennio; Unnerstall, Ulrich; Gaul, Ulrike & Gompel, Nicolas
-
(2019) ATAC-seq reveals regional differences in enhancer accessibility during the establishment of spatial coordinates in the Drosophila blastoderm. Genome Research, 29(5): 771-783
Bozek, Marta; Cortini, Roberto; Storti, Andrea Ennio; Unnerstall, Ulrich; Gaul, Ulrike & Gompel, Nicolas
-
(2019). Correlation of mRNA delivery timing and protein expression in lipid-based transfection. bioRxiv
Reiser, A.; Woschée, D.; Mehrotra, N.; Krzysztoń, R.; Strey, H. H. & Rädler, J. O.
-
124-color super-resolution imaging by engineering DNA-PAINT blinking kinetics; Nano Letters (2019). 19(4): 2641-2646
Wade, Orsolya K.; Woehrstein, Johannes B.; Nickels, Philipp C.; Strauss, Sebastian; Stehr, Florian; Stein, Johannes; Schueder, Florian; Strauss, Maximilian T.; Ganji, Mahipal; Schnitzbauer, Joerg; Grabmayr, Heinrich; Yin, Peng; Schwille, Petra & Jungmann, Ralf
-
A deep proteome and transcriptome abundance atlas of 29 healthy human tissues, Mol. Syst. Biol. 2019
Wang, Dongxue; Eraslan, Basak; Wieland, Thomas; Hallström, Björn; Hopf, Thomas; Zolg, Daniel Paul; Zecha, Jana; Asplund, Anna; Li, Li‐hua; Meng, Chen; Frejno, Martin; Schmidt, Tobias; Schnatbaum, Karsten; Wilhelm, Mathias; Ponten, Frederik; Uhlen, Mathias; Gagneur, Julien; Hahne, Hannes & Kuster, Bernhard
-
CAGI5 splicing challenge: Improved exon skipping and intron retention predictions with MMSplice, Human Mutation, 2019
Cheng, Jun; Çelik, Muhammed Hasan; Nguyen, Thi Yen Duong; Avsec, Žiga & Gagneur, Julien
-
Concepts and limitations for learning developmental trajectories from single cell genomics, Development 2019 146: dev170506
Tritschler, Sophie; Büttner, Maren; Fischer, David S.; Lange, Marius; Bergen, Volker; Lickert, Heiko & Theis, Fabian J.
-
Continuous nonenzymatic cross-replication of DNA strands with in situ activated DNA oligonucleotides Chemical Science 10, 5807 – 5814
Edeleva, Evgeniia; Salditt, Annalena; Stamp, Julian; Schwintek, Philipp; Boekhoven, Job & Braun, Dieter
-
Deep learning: new computational modelling techniques for genomics, Nature Reviews Genetics, 20, 389–403 (2019)
Eraslan, Gökcen; Avsec, Žiga; Gagneur, Julien & Theis, Fabian J.
-
Design of Sealable Custom-Shaped Cell Mimicries Based on Self- Assembled Monolayers on CYTOP Polymer, ACS Appl. Mater. Interfaces 2019, 11, 21372−21380
Eto, Hiromune; Soga, Naoki; Franquelim, Henri G.; Glock, Philipp; Khmelinskaia, Alena; Kai, Lei; Heymann, Michael; Noji, Hiroyuki & Schwille, Petra
-
Dynamic pseudo-time warping of complex single-cell trajectories; Research in Computational Molecular Biology. RECOMB 2019. Lecture Notes in Computer Science
Do, Van Hoan; Blažević, Mislav; Monteagudo, Pablo; Borozan, Luka; Elbassioni, Khaled; Laue, Sören; Ringeling, Francisca Rojas; Matijević, Domagoj & Canzar, Stefan
-
Flat-top TIRF illumination boosts DNA-PAINT imaging and quantification, Nature Communications, (2019). 10: 1268
Stehr, Florian; Stein, Johannes; Schueder, Florian; Schwille, Petra & Jungmann, Ralf
-
Fuzzy Interactions Form and Shape the Histone Transport Complex.; Mol Cell. 2019 Mar 21;73(6):1191-1203.e6
Ivic, Nives; Potocnjak, Mia; Solis-Mezarino, Victor; Herzog, Franz; Bilokapic, Silvija & Halic, Mario
-
High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy, J Vis Exp. 2019 Feb 7; (144)
Jung, Christophe; Schnepf, Max; Bandilla, Peter; Unnerstall, Ulrich & Gaul, Ulrike
-
Inferring population dynamics from single-cell RNA-sequencing time series data, Nature Biotechnology, 37, 461–468 (2019)
Fischer, David S.; Fiedler, Anna K.; Kernfeld, Eric M.; Genga, Ryan M. J.; Bastidas-Ponce, Aimée; Bakhti, Mostafa; Lickert, Heiko; Hasenauer, Jan; Maehr, Rene & Theis, Fabian J.
-
Measuring and Interpreting Oxygen Consumption Rates in Whole Fly Head Segments
Dietz, Louisa Jutta; Venkatasubramani, Anuroop Venkateswaran; Müller-Eigner, Annika; Hrabe de Angelis, Martin; Imhof, Axel; Becker, Lore & Peleg, Shahaf
-
MMSplice: modular modeling improves the predictions of genetic variant effects on splicing, Genome Biol. 2019
Cheng, Jun; Nguyen, Thi Yen Duong; Cygan, Kamil J.; Çelik, Muhammed Hasan; Fairbrother, William G.; Avsec, žiga & Gagneur, Julien
-
Multi-omics insights into functional alterations of the liver in insulin-deficient diabetes mellitus
Backman, Mattias; Flenkenthaler, Florian; Blutke, Andreas; Dahlhoff, Maik; Ländström, Erik; Renner, Simone; Philippou-Massier, Julia; Krebs, Stefan; Rathkolb, Birgit; Prehn, Cornelia; Grzybek, Michal; Coskun, Ünal; Rothe, Michael; Adamski, Jerzy; de Angelis, Martin Hrabĕ; Wanke, Rüdiger; Fröhlich, Thomas; Arnold, Georg J.; Blum, Helmut; ... & Wolf, Eckhard
-
Progressive dosage compensation during Drosophila embryogenesis is reflected by gene arrangement, EMBO reports (2019)e48138
Prayitno, Khairunnadiya; Schauer, Tamás; Regnard, Catherine & Becker, Peter B.
-
Quantification and discovery of sequence determinants of protein per mRNA amount in 29 human tissues, Mol. Syst. Biol. 2019
Eraslan, Basak; Wang, Dongxue; Gusic, Mirjana; Prokisch, Holger; Hallström, Björn M; Uhlén, Mathias; Asplund, Anna; Pontén, Frederik; Wieland, Thomas; Hopf, Thomas; Hahne, Hannes; Kuster, Bernhard & Gagneur, Julien
-
Reconstitution of the human SRP system and quantitative and systematic analysis of its ribosome interactions; Nucleic Acids Res. 2019 Apr 8;47(6):3184-3196
Wild, Klemens; Juaire, Keven D; Soni, Komal; Shanmuganathan, Vivekanandan; Hendricks, Astrid; Segnitz, Bernd; Beckmann, Roland & Sinning, Irmgard
-
Single Particle Tracking and Super-Resolution Imaging of Membrane-Assisted Stop-and-Go Diffusion and Lattice Assembly of DNA Origami; ACS Nano, 2019, 132, 996-1002
Kempter, Susanne; Khmelinskaia, Alena; Strauss, Maximilian T.; Schwille, Petra; Jungmann, Ralf; Liedl, Tim & Bae, Wooli
-
Stochastic nonlinear dynamics of confined cell migration in two-state systems. Nature Physics 15, 595–601 (2019)
Brückner, David B.; Fink, Alexandra; Schreiber, Christoph; Röttgermann, Peter J. F.; Rädler, Joachim O. & Broedersz, Chase P.
-
Structural and mutational analysis of the ribosome-arresting human XBP1u, Elife. 2019 Jun 27; 8
Shanmuganathan, Vivekanandan; Schiller, Nina; Magoulopoulou, Anastasia; Cheng, Jingdong; Braunger, Katharina; Cymer, Florian; Berninghausen, Otto; Beatrix, Birgitta; Kohno, Kenji; von Heijne, Gunnar & Beckmann, Roland
-
Structure and function of Vms1 and Arb1 in RQC and mitochondrial proteome homeostasis, Nature, 570, 538–542 (2019)
Su, Ting; Izawa, Toshiaki; Thoms, Matthias; Yamashita, Yui; Cheng, Jingdong; Berninghausen, Otto; Hartl, F. Ulrich; Inada, Toshifumi; Neupert, Walter & Beckmann, Roland
-
The COMA complex interacts with Cse4 and positions Sli15/Ipl1 at the budding yeast inner kinetochore.; Elife. 2019 May 21;8
Fischböck-Halwachs, Josef; Singh, Sylvia; Potocnjak, Mia; Hagemann, Götz; Solis-Mezarino, Victor; Woike, Stephan; Ghodgaonkar-Steger, Medini; Weissmann, Florian; Gallego, Laura D; Rojas, Julie; Andreani, Jessica; Köhler, Alwin & Herzog, Franz
-
The Kipoi repository accelerates community exchange and reuse of predictive models for genomics, Nature biotechnology, 2019
Avsec, Žiga; Kreuzhuber, Roman; Israeli, Johnny; Xu, Nancy; Cheng, Jun; Shrikumar, Avanti; Banerjee, Abhimanyu; Kim, Daniel S.; Beier, Thorsten; Urban, Lara; Kundaje, Anshul; Stegle, Oliver & Gagneur, Julien
-
Boosting Functional Response Models for Location, Scale and Shape with an Application to Bacterial Competition; arXiv:1809.09881
Stöcker, Almond; Brockhaus, Sarah; Schaffer, Sophia Anna; Bronk, Benedikt von; Opitz, Madeleine & Greven, Sonja
