- 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
