Systems Biology University of Freiburg
  Group | Curriculum Vitae | Software | Publications

Marcus Rosenblatt

Faculty of Mathematics and Physics
Institute of Physics
University of Freiburg
Hermann-Herder-Str. 3
79104 Freiburg i.Br.

E-mail: marcus.rosenblatt -at-
E-mail (private): marcus.rosenblatt -at-
Phone: +49 761 203 8530
Office: Physics Highrise 209
- Solution methods to parameter estimation in ODEs
- Steady-state solutions for ODE systems
- Quasi-steady-state approximations for time separation in ODE models
- Sensitization of interferon alpha signaling
- Zebrafish gene expression and zygotic development
- Bridging the gap between population-based ODE models and single cells
- From ODE models towards Quantitative Systems Pharmacology (QSP)

- dMod (Dynamic Modeling Framework for Parameter Estimation in R, CRAN or Github)
- InvasionCorrection (R Package for Correction of 3D Invasion Essay Data, CRAN)
- AlyssaPetit (Analytical Steady States for Parameter Estimation, based on Python3, Github)
- RNAsense (R Package for Analyzing Time Resolved RNAseq Data, Bioconductor or Github, Thanks to Meijang Gao for the explanation video!)

(08/2022) Kemmer S, Bang S, Rosenblatt M, Timmer J and Kaschek D
BlotIt—Optimal alignment of Western blot and qPCR experiments
PLoS One
(05/2022) Hiemstra S, Fehling-Kaschek M, Kuijper IA, Bischoff LJM, Wijaya LS, Rosenblatt M, Esselik J, van Egmond A, Mos J, Beltman JB, Timmer J, van de Water B, Kaschek D
Dynamic modeling of Nrf2 pathway activation in liver cells after toxicant exposure
Scientific Reports
(02/2022) Gao M, Veil M, Rosenblatt M, Riesle AJ, Gebhard A, Hass H, Buryanova L, Yampolsky LY, Grüning B, Ulianov S, Timmer J and Onichtchouk D
Pluripotency factors determine gene expression repertoire at zygotic genome activation
Nature Communications
(03/2021) Wieland FG, Hauber AL, Rosenblatt M, Tönsing C, Timmer J
On Structural and Practical Identifiability
Current Opinion in Systems Biology
(01/2021) Schmiester L, Schälte Y, Bergmann FT, Camba T, Dudkin E, Egert J, Fröhlich F, Furhmann L, Hauber AL, Kemmer S, Lakrisenko P, Loos C, Merkt S, Pathirana D, Raimúndez E, Refisch L, Rosenblatt M, Stapor PL, Städter P, Wang D, Wieland FG, Banga JR, Timmer J, Villaverde AF, Sahle S, Kreutz C, Hasenauer J and Weindl D
PEtab -- Interoperable Specification of Parameter Estimation Problems in Systems Biology
PLoS Computational Biology
(06/2020) Kok F, Rosenblatt M, Teusel M, Nizharadze T, Magalhaes VG, Dächert C, Maiwald T, Vlasov A, Wäsch M, Tyufekchieva S, Hoffmann K, Damm G, Seehofer D, Boettler T, Binder M, Timmer J, Schilling M and Klingmüller U
Disentangling Molecular Mechanisms Regulating Sensitization of Interferon Alpha Signal Transduction
Molecular Systems Biology
(04/2019) Kaschek D, Mader W, Fehling-Kaschek M, Rosenblatt M and Timmer J
Dynamic Modeling, Parameter Estimation and Uncertainty Analysis in R
Journal of Statistical Software
(06/2018) Dvornikov D, Schneider MA, Ohse S, Szczygieł M, Titkova I, Rosenblatt M, Muley T, Warth A, Herth FJ, Dienemann H, Thomas M, Timmer J, Schilling M, Busch H, Boerries M, Meister M and Klingmüller U
Expression Ratio of the TGFβ-Inducible Gene MYO10 is Prognostic for Overall Survival of Squamous Cell Lung Cancer Patients and Predicts Chemotherapy Response
Scientific Reports 2018, 8: 9517
(05/2016) Rosenblatt M, Timmer J and Kaschek D
Customized Steady-State Constraints for Parameter Estimation in Non-Linear Differential Equations Models
Frontiers in Cell and Developmental Biology 2016, 4:41
(08/2013) Kornilov O, Eckstein M, Rosenblatt M, Schulz C P, Motomura K, Rouzée A, Klei J, Foucar L, Siano M, Lübcke A, Schapper F, Johnsson P, Holland DMP, Schlathölter T, Marchenko T, Düsterer S, Ueda K, Vrakking MJJ and Frasinski LJ
Coulomb Explosion of Diatomic Molecules in Intense XUV Fields Mapped by Partial Covariance
Journal of Physics B: At. Mol. Opt. Phys. 46 164028

(10/2019) Coulibaly A, Bettendorf A, Kostina E, Figueiredo AS, Velasquez SY, Bock HG, Thiel M, Lindner HA and Barbarossa MV
Interleukin-15 Signaling in HIF-1α Regulation in Natural Killer Cells, Insights Through Mathematical Models
Frontiers in Immunology 2019, 10: 2401

Curriculum Vitae
since 01/2022
Parental Leave
since 04/2021
PostDoc in the Group of Prof. Dr. Jens Timmer
09/2014 - 04/2021
PhD student in the Group of Prof. Dr. Jens Timmer
12/2019 - 05/2020
Internship at IntiQuan GmbH
11/2017 - 05/2018
Internship at Walter and Eliza Hall Institute of Medical Research (WEHI), Structural Biology Lab of Prof. Tony Burgess, Melbourne, Victoria, Australia
04/2013 - 04/2014
Master thesis in the group of Prof. Dr. Jens Timmer
10/2011 - 04/2014
Graduate student in physics at Albert-Ludwigs-Universität Freiburg
04/2011 - 07/2011
Bachelor thesis at Max-Born-Institut Berlin
09/2010 - 03/2011
Exchange student in physics at Universidad Autónoma de Madrid, Spain
10/2008 - 07/2011 Undergraduate student in physics at Freie Universität Berlin
09/2007 - 06/2008 Civilian service at Kindergarten Spatzennest, Chemnitz
06/2007 Abitur at Johannes-Kepler Gymnasium , Chemnitz
05/1989 Born in Karl-Marx-Stadt (Chemnitz)