Daniel Franke

Senior Computational Scientist

Address

Tel: +49 40 89902 244
Fax: +49 40 89902 149
franke@embl-hamburg.de

Biography

Publications

• ATSAS 3.0: expanded functionality and new tools for small-angle scattering data analysis Manalastas-Cantos, K., Konarev, P.V., Hajizadeh, N.R., Kikhney, A.G., Petoukhov, M.V., Molodenskiy, D.S., Panjkovich, A., Mertens, H.D.T., Gruzinov, A., Borges, C., Jeffries, C.M., Svergun, D.I., Franke, D. J Appl Cryst. 2021. 54:343–355
• Simulation of small-angle X-ray scattering data of biological macromolecules in solution Franke, D., Hajizadeh, N.R., Svergun, D.I. J Appl Cryst. 2020. 53:536-539
• Consensus Bayesian assessment of protein molecular mass from solution X-ray scattering data Hajizadeh, N.R., Franke, D., Jeffries, C.M., Svergun, D.I. Scientific Reports. 2018. 8:7204
• Machine Learning Methods for X-ray Scattering Data Analysis from Biomacromolecular Solutions Franke, D., Jeffries, C.M., Svergun, D.I. Biophys J. 2018. 114:2485-2492
• Integrated Beamline Control and Data Acquisition for Small Angle X-ray Scattering at the P12 BioSAXS Beamline at PETRAIII Storage Ring DESY Hajizadeh, N.R., Franke, D., Svergun, D.I. J Synch Rad. 2018. 25:906-914
• ATSAS 2.8: a comprehensive data analysis suite for small-angle scattering from macromolecular solutions Franke, D., Petoukhov, M.V., Konarev, P.V., Panjkovich, A., Tuukkanen, A., Mertens, H.D.T., Kikhney, A.G., Hajizadeh, N.R., Franklin, J.M., Jeffries, C.M., Svergun, D.I. J Appl Cryst. 2017. 50:1212-1225
• Automated Pipeline for Purification, Biophysical and X-Ray Analysis of Biomacromolecular Solutions Graewert, M.A., Franke, D., Jeffries, C.M., Blanchet, C., Ruskule, D., Kuhle, K., Flieger, A., Schaefer, B., Tartsch, B., Meijers, R. and Svergun, D.I. Scientific Reports. 2015. 5:10734
• Correlation Map, a goodness-of-fit test for one-dimensional X-ray scattering spectra Franke, D., Jeffries, C.M. and Svergun, D.I. Nat Meth. 2015. 12:419-422
• Synchrotron Small-Angle X-Ray Scattering on Biological Macromolecules in Solution Franke, D. and Svergun D.I. Synchrotron Light Sources and Free-Electron Lasers 1:25
• Versatile sample environments and automation for biological solution X-ray scattering experiments at the P12 beamline (Petra-3, DESY) Blanchet, C.E., Spilotros, A., Schwemmer, F., Graewert, M.A., Kikhney, A.G., Jeffries, C.M., Franke, D., Mark, D., Zengerle, R., Cipriani, F., Fiedler, S., Roessle, M and Svergun, D.I. J Appl Cryst. 2015. 48:431-443
• ISPyB for BioSAXS, the gateway to user autonomy in solution scattering experiments De Maria Antolinos, A., Pernot, P., Brennich, M.E., Kieffer, J., Bowler, M.W., Delageniere, S., Ohlsson, S., Malbet Monaco, S., Ashton, A., Franke, D., Svergun, D.I., McSweeney, S., Gordon, E. and Round, A. Acta Cryst D. 2015. 71:76-85
• WeNMR: Structural Biology on the Grid T.A. Wassenaar, M. van Dijk, N. Loureiro-Ferreira, G. van der Schot, S.J. de Vries, C. Schmitz, J. van der Zwan, R. Boelens, A. Giachetti, L. Ferella, A. Rosato, I. Bertini, T. Herrmann, H.R.A. Jonker, A. Bagaria, V. Jaravine, P. Guntert, H. Schwalbe, W.F. Vranken, J.F. Doreleijers, G. Vriend, G.W. Vuister, D. Franke, A. Kikhney, D.I. Svergun, R. Fogh, J. Ionides, E.D. Laue, C. Spronk, S. Jurka, M. Verlato, S. Badoer, S. Dal Pra, M. Mazzucato, E. Frizziero and A.M.J.J. Bonvin. J. Grid. Comp. 2012. 10:743-767.
• Automated Acquisition and Analysis of Small Angle X-ray Scattering Data. Franke, D., Kikhney, A.G. and Svergun, D.I. Nuc Inst Meth A. 2012. 689: 52-59
• Instrumental setup for high throughput solution scattering at the X33 beamline of EMBL-Hamburg. Blanchet, C.E., Zozulya, A.V., Kikhney, A.G., Franke, D., Konarev, P.V., Shang, W., Klaering, R., Robrahn, B., Hermes, C., Cipriani, F., Svergun, D.I and Roessle, M. J Appl Cryst. 2012. 45:489-495
• New developments in the ATSAS program package for small-angle scattering data analysis. Petoukhov, M.V., Franke, D., Shkumatov, A.V., Tria, G., Kikhney, A.G., Gajda, M., Gorba, C., Mertens, H.D.T., Konarev, P.V. and Svergun, D.I. J Appl Cryst. 2012 45:342-350
• The dimer interface of the membrane type 1 matrix metalloproteinase hemopexin domain: crystal structure and biological functions. Tochowicz, A., Goettig, P., Evans, R., Visse, R., Shitomi, Y., Palmisano, R., Ito, N., Richter, K., Maskos, K., Franke, D., Svergun, D., Nagase, H., Bode, W. and Itoh, Y. J Biol Chem. 2011 Mar 4;286(9):7587-600
• An extensive comparison of quantitative trait Loci mapping methods. Kleensang, A., Franke, D., Alcais, A., Abel, L., Muller-Myhsok, B. and Ziegler, A. Hum Hered. 2010;69(3):202-11
• Structural and functional characterization of soluble endoglin receptor. Van Le, B., Franke, D., Svergun, D.I., Han, T., Hwang, H.Y. and Kim, K.K. Biochem Biophys Res Commun. 2009 Jun 12;383(4):386-91
• DAMMIF, a program for rapid ab-initio shape determination in small-angle scattering. Franke, D. and Svergun, D.I. J. Appl. Cryst. 2009 42 342-346
• Automated sample-changing robot for solution scattering experiments at the EMBL Hamburg SAXS station X33 A. R. Round, D. Franke, S. Moritz, R. Huchler, M. Fritsche, D. Malthan, R. Klaering, D. I. Svergun, D. and M. Roessle. J. Appl. Cryst. 2008/10 41 913-917
• Association of a polymorphism of the ACVRL1 gene with sporadic arteriovenous malformations of the central nervous system. Simon, M., Franke, D., Ludwig, M., Aliashkevich, A.F., Koster, G., Oldenburg, J., Bostrom, A., Ziegler, A. and Schramm, J. J Neurosurg. 2006 Jun;104(6):945-9.
• SIBSIM, quantitative phenotype simulation in extended pedigrees. Franke, D., Kleensang, A., Ziegler, A. GMS Med Inform Biom Epidemiol. 2006 2(1)
• Haplotype-sharing analysis for alcohol dependence based on quantitative traits and the Mantel statistic. Kleesang, A., Franke, D., Konig, I.R. & Ziegler, A. BMC Genet. 2005 Dec 30;6 Suppl 1:S75
• Haseman-Elston weighted by marker informativity. Franke, D., Kleensang, A., Elston, R.C. and Ziegler, A. BMC Genet. 2005 Dec 30;6 Suppl 1:S50.
• Weighting affected sib pairs by marker informativity. Franke, D. and Ziegler, A. Am J Hum Genet. 2005 Aug;77(2):230-41
• On confidence intervals for genotype relative risks and attributable risks from case parent trio designs for candidate-gene studies. Franke, D., Philippi, A., Tores, F., Hager, J., Ziegler, A. & Konig, I.R. Hum Hered. 2005;60(2):81-8
• Commentary on: Generalized estimating equations for association structures: familial correlations of lipid profiles. Franke, D., Kastner, C. & Ziegler, A. Stat In Med 2004 23(6) 875-877