DR. CLEMENS MARTIN KREUTZ

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1 DR. CLEMENS MARTIN KREUTZ Weißtannenweg Breitnau, Germany Center for Biosystems Analysis (ZBSA) Center for Data Analysis and Modeling (FDM) Physics Departement Albert-Ludwigs University of Freiburg Hermann Herder Straße Freiburg, Germany PERSONAL INFORMATION Family status Married with Susanne Kreutz since May 19th, 2007 Children Thilo Kreutz, September 9th, 2005 Mischa Kreutz, March 2nd, 2007 Ida Kreutz, October 28th, 2010 Henri Kreutz, July 7th, 2012 Nationality German Date of birth December 17th, 1977 Place of birth Titisee-Neustadt, Germany CAREER SUMMARY Since 2012 PostDoc at the University of Freiburg, Germany PhD thesis at the University of Freiburg, Germany. Topic: Statistical approaches for Molecular and Systems Biology, grade summa cum laude Physics studies at the University of Freiburg, Germany. Intermediate diploma (corresponding to Bachelor s Degree of Physics), grade sehr gut, diploma (corresponding to a Master s Degree of Science), grade sehr gut Military servic Comprehensive Secondary School (Commercial high school) in Titisee-Neustadt, Abitur grade Secondary School in Titisee-Neustadt, mark Elementary School in Breitnau, 2nd year skipped. WORK EXPERIENCES Since 2007 Since 2002 Full position as scientic employee at Freiburg University. Supervision of the lectures in programming, optimisation, stochastic processes, data analysis, theoretical physics and practical courses in experimental physics Partly position as scientic employee at Freiburg University Scientific assistant and software development for the company Seleon Scientific assistant at university hospital of Freiburg and Freiburg Material Research Center (FMF) Employee at consulting service of the computer center of the university Part time job in the public service of the communities Breitnau and Lenzkirch Temporary job in a small trading company One week laboratory in a financial institute.

2 RESEARCH SUMMARY Mathematical modelling of cellular signal transduction (Insulin signalling, Apoptosis) Experimental design Statistics Analysis of gene expression data (microarrays, high-throughput sequencing) Analysis of protein quantification assays (immunoblotting) Analysis of flow cytometry data FUNCTIONAL SKILLS Programming Languages Mathematics Further skills R, Matlab, C, C++, C#, Delphi, Perl German, English, very basics in Russian and French Statistics, parameter estimation, nonlinear dynamics, control theory, model identification, statistical tests, physics and mathematical applications Motivation and ambition HOBBIES Family, building my house, reading, lifeguard, and playing soccer including coaching of youth teams. SCIENTIFIC PUBLICATIONS Gene expression/dna microarrays: (1) S. Zellmer, W. Schmidt-Heck, A. Bauer, C. Meyer, T. Lehmann, T. Sparna, P. Godoy, P. Amin, W. Schormann, E. Bedawy, S. Hammad, C. Kern, C. Kreutz, J. Timmer, G. Walz, F. von Weizsäcker, P. Thürmann, S. Dooley, I. Merfort, R. Guthke, J. Hengstler, R. Gebhardt (2010). The transcription factors ETF, E2F and SP-1 are involved in cytokine-independent proliferation of murine hepatocytes. HEPATOLOGY, 52(6): (2) S. Lassmann, C. Kreutz, A. Schoepflin, U. Hopt, J. Timmer and M. Werner (2009). A novel approach for reliable microarray analysis of microdissected tumor cells from formalin-fixed and paraffin-embedded colorectal cancer resection specimens. JOURNAL OF MOLECULAR MEDICINE, 87: (3) B. Rumberger, C. Kreutz, Ch. Nickel, M. Klein, S. Lagoutte, S. Teschner, J. Timmer, P. Gerke, G. Walz, J. Donauer (2009). Combination of Immunosuppressive Drugs Leaves Specific Fingerprint on Gene Expression in-vitro. IMMUNOPHARMACOLOGY AND IMMUNOTOXICOLOGY, (4) K. Bartholomé, C. Kreutz, and J. Timmer (2009). Estimation of Gene Induction Enables a Relevance-based Ranking of Gene Sets. JOURNAL OF COMPUTATIONAL BIOLOGY, 16: (5) B. Rumberger, O. Vonend, C. Kreutz, J. Wilpert, J. Donauer, K. Amann, R. Rohrbach, J. Timmer, G. Walz, P. Gerke (2007). cdna microarray analysis of adaptive changes after renal ablation in a sclerosisresistant mouse strain. KIDNEY & BLOOD PRESSURE RESEARCH, 30 (6): (6) M. Lindenmeyer, C. Kern, T. Sparna, J. Donauer, J. Wilpert, J. Schwager, D. Porath, C. Kreutz, J. Timmer, I. Merfort (2007). Microarray analysis reveals influence of the sesquiterpene lactone parthenolide on gene transcription profiles in human epithelial cells. LIFE SCIENCES, 80 (17): (7) D. Pfeifer, M. Pantic, I. Skatulla, J. Rawluk, C. Kreutz, U. Martens, P. Fisch, J. Timmer, H. Veelken (2007). Genome-wide analysis of DNA copy number changes and LOH in CLL using high-density SNP arrays. BLOOD, 109 (3): (8) G. Schieren, B. Rumberger, M. Klein, C. Kreutz, J. Wilpert, M. Geyer, D. Faller, J. Timmer, I. Quack, L. Rump, G. Walz, J. Donauer (2006). Gene profiling of polycystic kidneys. NEPHROLOGY DIALYSIS TRANSPLANTATION, 21 (7): (9) X. Fang, M. Zeisel, J. Wilpert, B. Gissler, R. Thimme, C. Kreutz, T. Maiwald, J. Timmer, W. Kern, J. Donauer, M. Geyer, G. Walz, E. Depla, F. von Weizsacker, H. Blum, T. Baumert (2006). Host cell responses induced by hepatitis C virus binding. HEPATOLOGY, 43 (6): (10) P. Goerttler, C. Kreutz, J. Donauer, D. Faller, T. Maiwald, E. März, B. Rumberger, T. Sparna, A. Schmitt- Gräff, J. Wilpert, J. Timmer, G. Walz, HL. Pahl (2005). Gene expression profiling in polycythaemia vera: overexpression of transcription factor NF-E2. BRITISH JOURNAL OF HAEMATOLOGY, 129 (1):

3 Western blotting: (11) C. Kreutz, M. M. Bartolome-Rodriguez, T. Maiwald, M. Seidl, H. E. Blum, L. Mohr, J. Timmer (2007) An error model for protein quantification. BIOINFORMATICS, 23 (20): (12) M. Schilling, T. Maiwald, S. Bohl, M. Kollmann, C. Kreutz, J. Timmer, U. Klingmüller (2005). Quantitative data generation for systems biology: the impact of randomisation, calibrators and normalisers. IEE PROCEEDINGS SYSTEMS BIOLOGY, 152 (4): (13) M. Schilling, T. Maiwald, S. Bohl, M. Kollmann, C. Kreutz, J. Timmer, U. Klingmüller (2005). Computational processing and error reduction strategies for standardized quantitative data in biological networks. FEBS JOURNAL, 272 (24): Experimental design: (14) C. Kreutz, and J. Timmer (2009). Systems Biology: Experimental Design. FEBS JOURNAL, 276: (15) U. Klingmüller, A. Bauer, S. Bohl, P. Nickel, K. Breitkopf, S. Dooley, S. Zellmer, C. Kern, I. Merfort, T. Sparna, J. Donauer, G. Walz, M. Geyer, C. Kreutz, M. Hermes, F. Götschel, A. Hecht, D. Walter, Egger, K. Neubert, C. Borner, M. Brulport, W. Schormann, C. Sauer, F. Baumann, R. Preiss, S. MacNelly, P. Godoy, E. Wiercinska, L. Ciuclan, J. Edelmann, K. Zeilinger, M. Heinrich, U. Zanger, R. Gebhardt, T. Maiwald, R. Heinrich, J. Timmer, F. von Weizsacker, J. Hengstler (2006). Primary mouse hepatocytes for systems biology approaches: a standardized in vitro system for modelling of signal transduction pathways. IEE PROCEEDINGS SYSTEMS BIOLOGY, 153 (6): (16) T. Maiwald, C. Kreutz, A. Pfeifer, S. Bohl, U. Klingmüller, J. Timmer (2007). Dynamic pathway modeling: Feasibility analysis and optimal experimental design. ANNALS OF THE NEW YORK ACADEMY OF SCIENCES, 1115: (17) B. Steiert, A. Raue, J. Timmer, C. Kreutz Experimental design for parameter estimation of gene regulatory networks. PLoS ONE 2012; 7, e Dynamic modelling methodology: (18) A. Raue, C. Kreutz, T. Maiwald, U. Klingmüller, J. Timmer (2011). Addressing Parameter Identifiability by Model-Based Experimentation. IET SYSTEMS BIOLOGY, 5(2): (19) A. Raue, C. Kreutz, T. Maiwald, J. Bachmann, M. Schilling, U. Klingmüller, J. Timmer (2009). Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood. BIOINFORMATICS. 25(15): (20) S. Hengl, C. Kreutz, J. Timmer, T. Maiwald (2007) Data-based identifiability analysis of non-linear dynamical models. BIOINFORMATICS, 23 (19): (21) C. Kreutz, A. Raue, J. Timmer. Title: Likelihood based observability analysis and confidence intervals for predictions of dynamic models. BMC Systems Biology 2012; 6; doi: / Preprint version: (22) Schelker M, Raue A, Timmer J and Kreutz C Comprehensive estimation of input signals and dynamical parameters in biochemical reaction networks. Bioinformatics, 28(18), i522-i528, (23) A. Raue, C. Kreutz, F. Theis, J. Timmer. Joining Forces of Bayesian and Frequentist Methodology: A Study for Inference in the Presence of Non-Identifiability. Phil. Trans. Roy. Soc. A, 371, , (24) Kreutz C, Raue A, Kaschek D, and Timmer J. Profile Likelihood in Systems Biology. FEBS Journal, 2013; (25) Raue A, Schilling M, Bachmann J, Matteson A, Schelker M, Kaschek D, Hug S, Kreutz C, Harms BD, Theis F, Klingmueller U and Timmer J. Lessons Learned from Quantitative Dynamical Modeling in Systems Biology. PLOS ONE 8(9), e74335, Dynamic modeling applications: (26) J. Bachmann, A. Raue, M. Schilling, M. Bohm, C. Kreutz, D. Kaschek, H. Busch, N. Gretz, W. Lehmann, J. Timmer, U. Klingmüller (2011). Division of labor by dual feedback regulators controls JAK2/STAT5 signaling over broad ligand range. MOLECULAR SYSTEMS BIOLOGY, 7: (27) M. Schilling, T. Maiwald, S. Hengl, D. Winter, C. Kreutz, W. Kolch, W. Lehmann, J. Timmer, U. Klingmüller (2009). Theoretical and experimental analysis links isoform-specific ERK signalling to cell fate decisions. MOLECULAR SYSTEMS BIOLOGY, 5: (28) K. Sa Ferreira, C. Kreutz, S. MacNelly, K. Neubert, A. Haber, M. Bogyo, J. Timmer, C. Borner. Caspase-3 feeds back on caspase-8, Bid and XIAP in type I Fas signaling in primary mouse hepatocytes. Apoptosis 2012; 17(5), Control theory.

4 (29) C. Kreutz, J. Honerkamp (2005). Controlling the continuos positive airway pressure-device using partial observable Markov decision processes MODELLING, SIMULATION AND OPTIMIZATION OF COM- PLEX PROCESSES, Bioinformatics. (30) C. Kreutz, J.S. Gehring, D. Lang, R. Reski, J. Timmer, S.A. Rensing TSSi - An R package for transcription start site identification from 5 mrna tag data. Bioinformatics Biomedical applications. (31) A. Yalcin, C. Kreutz, D. Pfeifer, M. Abdelkarim, G. Klaus, J. Timmer, M. Luebbert, B. Hackanson MeDIP coupled with a promoter tiling array as a platform to investigate global DNA methylation patterns in AML cells. Leukemia Research, (32) K. Aumann, A.-V. Frey, A.M. May, D. Hauschke, C. Kreutz, J.P. Marx, J. Timmer, M. Werner, H.L. Pahl Differenzialdiagnose myelproliferativer Neoplasien Der Pathologe 34: , 2013.

5 Publicly available software: (1) C. Kreutz, J.S. Gehring, D. Lang, R. Reski, J. Timmer, S.A. Rensing (2011). TSSi: Transcription Start Sites Identification from 5 mrna tag data. Bioconductor R-package. (2) J.S. Gehring, C. Kreutz, J. Timmer (2009). les: Identifying Differential Effects in Tiling Microarray Data. Bioconductor R-package. (3) J.S. Gehring, K. Bartholome, C. Kreutz, J. Timmer (2007). GSRI: Gene Set Regulation Index. Bioconductor R-package. Awards: (1) Team crux: C. Kreutz, A. Raue, B. Steiert, J. Timmer. Dialogue for Reverse Engineering Assessments and Methods (DREAM6): Parameter Estimation and Experimental Design Challenge. Best performing participants 2011.

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