GSC 1006:  Graduate School of Quantitative Biosciences Munich (QBM)

• Subject Area: Basic Research in Biology and Medicine
• Term: from 2012 to 2019
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 194407719

• Final Report Year: 2020

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

• (2013). Transcriptome surveillance by selective termination of noncoding RNA synthesis. Cell 155, 1075-1087
  Schulz, D., Schwalb, B., Kiesel, A., Baejen, C., Torkler, P., Gagneur, J., Soeding, J., and Cramer, P.
  
• (2014). ATP puts the brake on DNA double‐strand break repair. Bioessays 36, 1170-1178
  Hopfner, K.P.
  
• (2014). Genome activation in bovine embryos: review of the literature and new insights from RNA sequencing experiments. Animal reproduction science 149, 46-58
  Graf, A., Krebs, S., Heininen-Brown, M., Zakhartchenko, V., Blum, H., and Wolf, E.
  
• (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, F., Hross, S., Theis, F.J., and Hasenauer, J.
  
• (2014). RIG-I holds the CARDs in a game of self versus nonself. Molecular cell 55, 505-507
  Hopfner, K. P.
  
• (2014). Toward Spatially Regulated Division of Protocells: Insights into the E. coli Min System from in Vitro Studies. Life 4, 915-928
  Kretschmer, S., and Schwille, P.
  
• (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, F., Theis, F.J., and Hasenauer, J.
  
• (2015). Biallelic Mutations in NBAS Cause Recurrent Acute Liver Failure with Onset in Infancy. American journal of human genetics 97, 163-169
  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). destiny: diffusion maps for large-scale single-cell data in R. Bioinformatics
  Angerer, P., Haghverdi, L., Büttner, M., Theis, F.J., Marr, C., and Buettner, F.
  
• (2015). Marker-free detection of progenitor cell differentiation by analysis of Brownian motion in microwells. Integrative Biology 7, 178-183
  Sekhavati, F., Endele, M., Rappl, S., Marel, A.-K., Schroeder, T., and Rädler, J.O.
  
• (2015). Negative feedback buffers effects of regulatory variants. Molecular systems biology 11, 785
  Bader, D.M., Wilkening, S., Lin, G., Tekkedil, M.M., Dietrich, K., Steinmetz, L.M., and Gagneur, J.
  
• (2015). Re-Annotator: Annotation Pipeline for Microarray Probe Sequences. PloS one 10, e0139516
  Arloth, J., Bader, D.M., Röh, S., and Altmann, A.
  
• (2015). Rekonstitution biologischer Selbstorganisation in vitro. BIOspektrum 21, 148-150
  Kretschmer, S., and Schwille, P.
  
• (2015). Structure of a human translation termination complex. Nucleic acids research 43, 8615-8626
  Matheisl, S., Berninghausen, O., Becker, T., and Beckmann, R.
  
• (2015). Translational arrest by a prokaryotic signal recognition particle is mediated by RNA interactions. Nature structural & molecular biology 22, 767-773
  Beckert, B., Kedrov, A., Sohmen, D., Kempf, G., Wild, K., Sinning, I., Stahlberg, H., Wilson, D.N., and Beckmann, R.
  
• (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, M., Herzog, M., Greiss, F., Wolff, M., and Braun, D.
  
• (2016). Active Curved Polymers Form Vortex Patterns on Membranes. Phys Rev Lett 116
  Denk, J., Huber, L., Reithmann, E., and Frey, E.
  
• (2016). CERENA: ChEmical REaction Network Analyzer-A Toolbox for the Simulation and Analysis of Stochastic Chemical Kinetics. PloS one 11, e0146732
  Kazeroonian, A., Fröhlich, F., Raue, A., Theis, F.J., and Hasenauer, J.
  
• (2016). Chip-based platform for dynamic analysis of NK cell cytolysis mediated by a triplebody. Analyst 141, 2284-2295
  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). Chiral vortex dynamics on membranes is an intrinsic property of FtsZ, driven by GTP hydrolysis. bioRxiv
  Ramirez, D., Garcia-Soriano, D.A., Raso, A., Feingold, M., Rivas, G., and Schwille, P.
  
• (2016). DeepWAS: Directly integrating regulatory information into GWAS using deep learning supports master regulator MEF2C as risk factor for major depressive disorder. bioRxiv
  Eraslan, G., Arloth, J., Martins, J., Iurato, S., Czamara, D., Binder, E.B., Theis, F.J., and Mueller, N.S.
  
• (2016). Determinants of RNA metabolism in the Schizosaccharomyces pombe genome. Mol Syst Biol 12, 857
  Eser, P., Wachutka, L., Maier, K.C., Demel, C., Boroni, M., Iyer, S., Cramer, P., and Gagneur, J.
  
• (2016). Diffusion pseudotime robustly reconstructs lineage branching. Nature methods 13, 845-848
  Haghverdi, L., Büttner, M., Wolf, F.A., Buettner, F., and Theis, F.J.
  
• (2016). DNA nanotechnology and fluorescence applications. Current opinion in biotechnology 39, 41- 47
  Schlichthaerle, T., Strauss, M.T., Schueder, F., Woehrstein, J.B., and Jungmann, R.
  
• (2016). Dual-targeting triplebody 33-3-19 mediates selective lysis of biphenotypic CD19+ CD33+ leukemia cells. Oncotarget 7, 22579
  Roskopf, C.C., Braciak, T.A., Fenn, N.C., Kobold, S., Fey, G.H., Hopfner, K.-P., and Oduncu, F.S.
  
• (2016). Effect of anchor positioning on binding and diffusion of elongated 3D DNA nanostructures on lipid membranes. J Phys D Appl Phys 49
  Khmelinskaia, A., Franquelim, H.G., Petrov, E.P., and Schwille, P.
  
• (2016). Effects of shear flow on phase nucleation and crystallization. Physical Review E 93, 042803
  Mura, F., Zaccone., A.
  
• (2016). Inference for Stochastic Chemical Kinetics Using Moment Equations and System Size Expansion. Plos Comput Biol 12
  Fröhlich, F., Thomas, P., Kazeroonian, A., Theis, F.J., Grima, R., and Hasenauer, J.
  
• (2016). Parameter estimation for dynamical systems with discrete events and logical operations. Bioinformatics
  Fröhlich, F., Theis, F.J., Rädler, J.O., and Hasenauer, J.
  
• (2016). Pattern formation on membranes and its role in bacterial cell division. Current opinion in cell biology 38, 52-59
  Kretschmer, S., and Schwille, P.
  
• (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., and Jenne, D.E.
  
• (2016). Single-Molecule Imaging in Living Drosophila Embryos with Reflected Light-Sheet Microscopy. Biophys J 110, 939-946
  Greiss, F., Deligiannaki, M., Jung, C., Gaul, U., and Braun, D.
  
• (2016). Structure of the hypusinylated eukaryotic translation factor eIF-5A bound to the ribosome. Nucleic acids research 44, 1944- 1951
  Schmidt, C., Becker, T., Heuer, A., Braunger, K., Shanmuganathan, V., Pech, M., Berninghausen, O., Wilson, D.N., and Beckmann, R.
  
• (2016). The cryo-EM structure of a ribosome-Ski2-Ski3-Ski8 helicase complex. Science 354, 1431-1433
  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). TT-seq maps the human transient transcriptome. Science 352, 1225-1228
  Schwalb, B., Michel, M., Zacher, B., Fruhauf, K., Demel, C., Tresch, A., Gagneur, J., and Cramer, P.
  
• (2017). Assessment of batchcorrection methods for scRNA-seq data with a new test metric. bioRxiv, 200345
  Buttner, M., Miao, Z., Wolf, A., Teichmann, S.A., and Theis, F.J.
  
• (2017). Beyond pseudotime: Following T-cell maturation in single-cell RNAseq time series
  Fischer, D.S., Fiedler, A.K., Kernfeld, E., Genga, R.M., Hasenauer, J., Maehr, R., and Theis, F.J.
  
• (2017). Broken detailed balance and non-equilibrium dynamics in living systems
  Gnesotto, F., Mura, F., Gladrow, J., and Broedersz, C.P.
  
• (2017). CD40-signalling abrogates induction of RORγt(+) Treg cells by intestinal CD103(+) DCs and causes fatal colitis. Nature Communications 8, 14715
  Barthels, C., Ogrinc, A., Steyer, V., Meier, S., Simon, F., Wimmer, M., Blutke, A., Straub, T., Zimber-Strobl, U., Lutgens, E., et al.
  
• (2017). Chromosome topology guides the Drosophila Dosage Compensation Complex for target gene activation. EMBO reports 18, 1854-1868
  Schauer, T., Ghavi‐Helm, Y., Sexton, T., Albig, C., Regnard, C., Cavalli, G., Furlong, E.E., and Becker, P.B.
  
• (2017). Cis-regulatory elements explain most of the mRNA stability variation across genes in yeast. Rna 23, 1648-1659
  Cheng, J., Maier, K.C., Avsec, Z., Rus, P., and Gagneur, J.
  
• (2017). compleXView: a server for the interpretation of protein abundance and connectivity information to identify protein complexes. Nucleic acids research
  Solis-Mezarino, V., and Herzog, F.
  
• (2017). Control of lipid domain organization by a biomimetic contractile actomyosin cortex. eLife 6
  Vogel, S.K., Greiss, F., Khmelinskaia, A., and Schwille, P.
  
• (2017). Deciphering the molecular architecture of membrane contact sites by cryo-electron tomography. Biochimica et biophysica acta
  Collado, J., and Fernandez-Busnadiego, R.
  
• (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, B., Schaffer, S.A., Gotz, A., and Opitz, M.
  
• (2017). Efficient parameterization of large-scale mechanistic models enables drug response prediction for cancer cell lines. bioRxiv, 174094
  Froehlich, F., Kessler, T., Weindl, D., Shadrin, A., Schmiester, L., Hache, H., Muradyan, A., Schuette, M., Lim, J.-H., Heinig, M., et al.
  
• (2017). Emergence of life from trapped nucleotides? Non-equilibrium behavior of oligonucleotides in thermal gradients. Synlett 28, 56-63
  Agerschou, E.D., Mast, C.B., Braun, D.
  
• (2017). Exploiting ecology in drug pulse sequences in favour of population reduction. Plos Comput Biol 13, e1005747
  Bauer, M., Graf, I.R., Ngampruetikorn, V., Stephens, G.J., and Frey, E.
  
• (2017). Fast, background-free DNA-PAINT imaging using FRET-based probes. Nano letters 17, 6428-6434
  Auer, A., Strauss, M.T., Schlichthaerle, T., and Jungmann, R.
  
• (2017). Generic transport mechanisms for molecular traffic in cellular protrusions. Phys Rev Lett 118, 128101
  Graf, I.R., and Frey, E.
  
• (2017). Genetic diagnosis of Mendelian disorders via RNA sequencing. Nat Commun 8, 15824
  Kremer, L.S., Bader, D.M., Mertes, C., Kopajtich, R., Pichler, G., Iuso, A., Haack, T.B., Graf, E., Schwarzmayr, T., Terrile, C., et al.
  
• (2017). GenoGAM: genome-wide generalized additive models for ChIP-Seq analysis. Bioinformatics, btx150
  Stricker, G., Engelhardt, A., Schulz, D., Schmid, M., Tresch, A., and Gagneur, J.
  
• (2017). GenSSI 2.0: Multi-experiment structural identifiability analysis of SBML models. Bioinformatics
  Ligon, T.S., Fröhlich, F., Chi, O.T., Banga, J.R., Balsa-Canto, E., and Hasenauer, J.
  
• (2017). High-speed AFM reveals the inner workings of the MinDE protein oscillator. Nano letters
  Miyagi, A., Ramm, B., Schwille, P., and Scheuring, S.
  
• (2017). Identification of a plasma miRNA biomarker signature for allergic asthma: A translational approach. Allergy 72, 1962-1971
  Milger, K., Gotschke, J., Krause, L., Nathan, P., Alessandrini, F., Tufman, A., Fischer, R., Bartel, S., Theis, F.J., Behr, J., et al.
  
• (2017). In Situ Architecture and Cellular Interactions of PolyQ Inclusions. Cell 171, 179-187 e110
  Bäuerlein, F.J.B., Saha, I., Mishra, A., Kalemanov, M., Martínez-Sánchez, A., Klein, R., Dudanova, I., Hipp, M.S., Hartl, F.U., Baumeister, W., Fernández-Busnadiego, R.
  
• (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, S., Zieske, K., and Schwille, P.
  
• (2017). Matrix composition determines the dimensions of Bacillus subtilis NCIB 3610 biofilm colonies grown on LB agar. RSC Advances 7, 31886-31898
  Kesel, S., von Bronk, B., Falcon Garcia, C., Gotz, A., Lieleg, O., and Opitz, M.
  
• (2017). Mechanistic hierarchical population model identifies latent causes of cell-to-cell variability. bioRxiv, 171561
  Loos, C., Moeller, K., Fröhlich, F., Hucho, T., and Hasenauer, J.
  
• (2017). Microfluidic self-assembly of folate-targeted monomolecular siRNA-lipid nanoparticles. Nanoscale 9, 7442- 7453
  Krzyszton, R., Salem, B., Lee, D.J., Schwake, G., Wagner, E., Rädler, J.O.
  
• (2017). Model-based branching point detection in single-cell data by K-Branches clustering. Bioinformatics
  Chlis, N.K., Alexander Wolf, F., and Theis, F.J.
  
• (2017). Modeling positional effects of regulatory sequences with spline transformations increases prediction accuracy of deep neural networks. Bioinformatics
  Avsec, Z., Barekatain, M., Cheng, J., Gagneur, J.
  
• (2017). Multireference spectral library yields almost complete coverage of heterogeneous LC-MS/MS data sets. bioRxiv, 180448
  Ammar, C., Berchtold, E., Csaba, G., Schmidt, A., Imhof, A., and Zimmer, R.
  
• (2017). Optimal compartmentalization strategies for metabolic microcompartments. Biophys J 112, 767 – 779
  Hinzpeter, F., Gerland, U., Tostevin, F.
  
• (2017). Organs on chip approach: a tool to evaluate cancer-immune cells interactions. Sci Rep-Uk 7, 12737
  Biselli, E., Agliari, E., Barra, A., Bertani, F.R., Gerardino, A., De Ninno, A., Mencattini, A., Di Giuseppe, D., Mattei, F., Schiavoni, G., et al.
  
• (2017). PESTO: Parameter EStimation TOolbox. Bioinformatics
  Stapor, P., Weindl, D., Ballnus, B., Hug, S., Loos, C., Fiedler, A., Krause, S., Hroß, S., Fröhlich, F., and Hasenauer, J.
  
• (2017). Probing the cooperativity of binding networks with high-throughput thermophoresis. Analytical Chemistry 89 (4), 2592-2597
  Greiss, F., Kriegel, F., Braun, D.
  
• (2017). Scalable Inference of Ordinary Differential Equation Models of Biochemical Processes. arXiv preprint arXiv:171108079
  Fröhlich, F., Loos, C., and Hasenauer, J.
  
• (2017). Scalable parameter estimation for genome-scale biochemical reaction networks. Plos Comput Biol 13(1): e1005331
  Fröhlich, F., Kaltenbacher, B, Theis, F.J., Hasenauer, J.
  
• (2017). Sen1 has unique structural features grafted on the architecture of the Upf1-like helicase family. The EMBO journal 36, 1590-1604
  Leonaite, B., Han, Z., Basquin, J., Bonneau, F., Libri, D., Porrua, O., and Conti, E.
  
• (2017). Single cells make big data: New challenges and opportunities in transcriptomics. Current Opinion in Systems Biology 4, 85-91
  Angerer, P., Simon, L., Tritschler, S., Wolf, F.A., Fischer, D., and Theis, F.J.
  
• (2017). SIRPalpha-antibody fusion proteins stimulate phagocytosis and promote elimination of acute myeloid leukemia cells. Oncotarget 8, 11284-11301
  Ponce, L.P., Fenn, N.C., Moritz, N., Krupka, C., Kozik, J.H., Lauber, K., Subklewe, M., and Hopfner, K.P.
  
• (2017). Spt5 Plays Vital Roles in the Control of Sense and Antisense Transcription Elongation. Molecular cell 66, 77-88 e75
  Shetty, A., Kallgren, S.P., Demel, C., Maier, K.C., Spatt, D., Alver, B.H., Cramer, P., Park, P.J., and Winston, F.
  
• (2017). Super-resolution microscopy with DNA-PAINT. Nature protocols 12, 1198-1228
  Schnitzbauer, J., Strauss, M.T., Schlichthaerle, T., Schueder, F., and Jungmann, R.
  
• (2017). Systematic single-cell analysis provides new insights into heterogeneity and plasticity of the pancreas. Molecular metabolism 6, 974-990
  Tritschler, S., Theis, F.J., Lickert, H., and Böttcher, A.
  
• (2017). The Drosophila Dosage Compensation Complex activates target genes by chromosome looping within the active compartment. bioRxiv.
  Schauer, T., Ghavi-Helm, Y., Sexton, T., Albig, C., Regnard, C., Cavalli, G., Furlong, E.E.M., and Becker, P.B.
  
• (2017). The Drosophila speciation factor HMR localizes to genomic insulator sites. PloS one 12, e0171798
  Gerland, T.A., Sun, B., Smialowski, P., Lukacs, A., Thomae, A.W., and Imhof, A.
  
• (2017). The force-sensing peptide VemP employs extreme compaction and secondary structure formation to induce ribosomal stalling. eLife 6
  Su, T., Cheng, J., Sohmen, D., Hedman, R., Berninghausen, O., von Heijne, G., Wilson, D.N., and Beckmann, R.
  
• (2017). The Munich MIDY Pig Biobank – A unique resource for studying organ crosstalk in diabetes. Mol Metab 6, 931-940
  Blutke, A., Renner, S., Flenkenthaler, F., Backman, M., Haesner, S., Kemter, E., Landstrom, E., Braun-Reichhart, C., Albl, B., Streckel, E., et al.
  
• (2017). The PomXYZ Proteins Self-Organize on the Bacterial Nucleoid to Stimulate Cell Division. Developmental Cell 41, 299-314. e213
  Schumacher, D., Bergeler, S., Harms, A., Vonck, J., Huneke-Vogt, S., Frey, E., and Søgaard- Andersen, L.
  
• (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, N., Lauffer, F., Krause, L., Thomas, J., Atenhan, A., Franz, R., Roenneberg, S., Boehner, A., Jargosch, M., Batra, R., et al.
  
• (2017). TT-seq captures enhancer landscapes immediately after T-cell stimulation. Mol Syst Biol 13, 920
  Michel, M., Demel, C., Zacher, B., Schwalb, B., Krebs, S., Blum, H., Gagneur, J., and Cramer, P.
  
• (2017). Universelles Superauflösungs- Multiplexing durch DNA-Austausch. Angewandte Chemie 129, 4111-4114
  Schueder, F., Strauss, M.T., Hoerl, D., Schnitzbauer, J., Schlichthaerle, T., Strauss, S., Yin, P., Harz, H., Leonhardt, H., and Jungmann, R.
  
• (2017). Visualizing the Assembly Pathway of Nucleolar Pre-60S Ribosomes. Cell 171, 1599-1610. e1514
  Kater, L., Thoms, M., Barrio-Garcia, C., Cheng, J., Ismail, S., Ahmed, Y.L., Bange, G., Kressler, D., Berninghausen, O., Sinning, I., et al.
  
• 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, S., Dayem-Quere, M., Gusic, M., Chaussenot, A., Bannwarth, S., François, B., Genin, E.C., Fragaki, K., Volker-Touw, C.L.M., Vasnier, C., et al.
  
• (2018), Complex microbial systems across different levels of description, Physical Biology, 15, 5
  von Bronk, B., Götz, A. and Opitz, M.
  
• (2018). Altered Localization of Hybrid Incompatibility Proteins in Drosophila, Molecular Biology and Evolution, msz105
  Cooper, J.C., Lukacs, A., Reich, S., Schauer, T., Imhof, A., Phadnis, N.
  
• (2018). Benchmarking optimization methods for parameter estimation in large kinetic models. bioRxiv
  Villaverde, A.F., Froehlich, F., Weindl, D., Hasenauer, J., and Banga, J.R.
  
• (2018). Guiding 3D cell migration in deformed synthetic hydrogel microstructures. Soft matter 14, 2816 -2826
  Dietrich, M., Le Roy, H., Brückner, D.B., Engelke, H., Zantl, R., Rädler, J.O., and Broedersz, C.P.
  
• (2018). In Vitro Reconstitution of Self-Organizing Protein Patterns on Supported Lipid Bilayers J. Vis. Exp. (137). e58139
  Ramm, B., Glock, P., Schwille, P.
  
• (2018). Intricate structure of the interphase chromocenter revealed by the analysis of a factor involved in species formation
  Kochanova, N., Schauer, T., Mathias, G.P., Lukacs, A., Schmidt, A., Flatley, A., Schepers,A., Thomae, A.W., Imhof, A.
  
• (2018). Membrane sculpting by curved DNA origami scaffolds. Nat Commun 9, 811
  Franquelim, H.G., Khmelinskaia, A., Sobczak, J.P., Dietz, H., and Schwille, P.
  
• (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, J., Kretschmer, S., Halatek, J., Hartl, C., Schwille, P., and Frey, E.
  
• (2018). Modular modeling improves the predictions of genetic variant effects on splicing
  Cheng, J., Nguyen, T.Y.D., Cygan, K.J., Celik, M.H., Fairbrother, W.G., Avsec, Z., Gagneur, J.
  
• (2018). Multi-Experiment Nonlinear Mixed Effect Modeling of Single-Cell Translation Kinetics after Transfection
  Froehlich, F., Reiser, A., Fink, L., Woschee, D., Ligon, T., Theis, F., Raedler, J., and Hasenauer, J.
  
• (2018). Multi-experiment nonlinear mixed effect modeling of single-cell translation kinetics after transfection. npj Systems Biology and applications 4, Article number: 42
  Fröhlich, F., Reiser, A., Fink, L., Woschee, D., Ligon, T., Theis, F.J., Rädler, J.O., Hasenauer, J.
  
• (2018). Non-equilibrium scaling behaviour in driven soft biological assemblies. arXiv preprint arXiv:180302797
  Mura, F., Gradziuk, G., and Broedersz, C.P.
  
• (2018). OCR-Stats: Robust estimation and statistical testing of mitochondrial respiration activities using Seahorse XF Analyzer
  Yepez M, V.A., Kremer, L.S., Iuso, A., Gusic, M., Kopajtich, R., Konarikova, E., Nadel, A., Wachutka, L., Prokisch, H., and Gagneur, J.
  
• (2018). Optimization and uncertainty analysis of ODE models using second order adjoint sensitivity analysis. bioRxiv
  Stapor, P., Froehlich, F., and Hasenauer, J.
  
• (2018). Regulation of Pom cluster dynamics in Myxococcus xanthus
  Bergeler, S., and Frey, E.
  
• (2018). Reverse and forward engineering of protein pattern formation. Philosophical Transactions of the Royal Society B: Biological Sciences 373
  Kretschmer, S., Harrington, L., and Schwille, P.
  
• (2018). Self-organized system size oscillation of a stochastic lattice-gas model
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• (2018). Single Cell Microarrays Fabricated by Microscale Plasma-Initiated Protein Patterning (μPIPP). In Cell-Based Microarrays (Springer), pp. 41-54
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