Luty 7, 2013


Sensitivity Analysis
Nienałtowski, K., Jetka, T.,Komorowski, M.
To appear in Quantitative Biology: Theory, Computational Methods and Examples of Models, MIT press.

Experimental Design
Jetka, T., Nienałtowski, K., Komorowski, M.
To appear in Quantitative Biology: Theory, Computational Methods and Examples of Models, MIT press.

Nuclear translocation of STAT3 and NF-κB are independent of each other but NF-κB supports expression and activation of STAT3.
Martincuks, A., Andryka, K., Küster, A., Schmitz-Van de Leur, H., Komorowski, M., & Müller-Newen, G.
Cellular signalling, 32, 36-47.

Clustering reveals limits of parameter identifiability in multi-parameter models of biochemical dynamics.
Nienałtowski K, Włodarczyk M, Lipniacki T, Komorowski M.
BMC Systems Biology 9.1 (2015): 65.

Computational modeling of sphingolipid metabolism.
Wronowska W,Charzyńska A, Nienałtowski K, Gambin A.
BMC Systems Biology 9.1 (2015): 47.

Nitrogen and carbon status are integrated at the transcriptional level by the nitrogen regulator NtrC in vivo.
Schumacher J, Behrends V, Pan Z, Brown DR, Heydenreich F, Lewis MR, Bennett MH, Razzaghi B, Komorowski M, Barahona M, Stumpf MPH, Wigneshweraraj S, Bundy JG, Buck M.
mBio. 2013 Nov 4(6): e00881-13.

StochDecomp – Matlab package for noise decomposition in stochastic biochemical systems.
Jetka T., Charzynska A.,Gambin A., Stumpf M.P.H., Komorowski M.
Bioinformatics.  2013; doi: 10.1093/bioinformatics/btt631

Quantifying intrinsic and extrinsic noise in gene transcription using the linear noise approximation: an application to single cell data
Finkenstadt BF, Woodcock DJ, Komorowski M.,  Harper CV, Davis JRE, White MRH and Rand DA
Annals of Applied Statistics. 2013 (in press).

A hierarchical model of transcriptional dynamics allows robust estimation of transcription rates in populations of single cells with variable gene copy number.
Woodcock DJ, Vance KW, Komorowski M, Koentges G, Finkenstad B,  Rand DA
Bioinformatics. 2013 May 29 (12), 1519-1525

Decomposing Noise in Biochemical Signalling Systems Highlights the Role of Protein Degradation.
Komorowski M, Miekisz J, Stumpf MPH.
Biophys. J. 2013 Apr 16;104(8):1783-93.

Maximising the information content of experiments in systems biology
Liepe J, Filippi S, Komorowski M, Stumpf MPH,
PLOS Comp Biol. 2013 Feb 9(1), e1002888.

Mathematical modeling reveals the functional implications of the different nuclear shuttling rates of Erk1 and Erk2.
Harrington HA, Komorowski M, Beguerisse Díaz M, Ratto GM, Stumpf MPH,
Phys Biol. 2012 May 3;9(3):036001.

StochSens– matlab package for sensitivity analysis of stochastic chemical systems.
Komorowski M, Zurauskiene J, Stumpf MP.
Bioinformatics. 2012 March 28(5):731-3.

Sensitivity, robustness, and identifiability in stochastic chemical kinetics models.
Komorowski M, Costa MJ, Rand DA, Stumpf MP.
Proc Natl Acad Sci U S A. 2011 May 24;108(21):8645-50. Epub 2011 May 6.

Using a single fluorescent reporter gene to infer half-life of extrinsic noise and other parameters of gene expression.
Komorowski M, Finkenstädt B, Rand D.
Biophys J. 2010 Jun 16;98(12):2759-69.

Bayesian inference of biochemical kinetic parameters using the linear noise approximation.
Komorowski M, Finkenstädt B, Harper CV, Rand DA.
BMC Bioinformatics. 2009 Oct 19;10:343.

Translational repression contributes greater noise to gene expression than transcriptional repression.
Komorowski M, Miekisz J, Kierzek AM.
Biophys J. 2009 Jan;96(2):372-84.

Reconstruction of transcriptional dynamics from gene reporter data using differential equations.
Finkenstädt B, Heron EA, Komorowski M, Edwards K, Tang S, Harper CV, Davis JR, White MR, Millar AJ, Rand DA.
Bioinformatics. 2008 Dec 15;24(24):2901-7. Epub 2008 Oct 30


Analog nitrogen sensing in Escherichia coli enables high fidelity information processing.
Komorowski M, Schumacher J, Behrends V, Jetka T, Bennett MH, Ale A, Filippi S, Pinney JW, Bundy JG, Buck M, Stumpf MPH. Submitted. BioRxiv