2018

Villaverde A, Fröhlich F, Weindl D, Hasenauer J, Banga JR.
Benchmarking optimization methods for parameter estimation in large kinetic models.
Bioinformatics. 2018 Aug 24;bty736. doi.org/10.1093/bioinformatics/bty736. [ABSTRACT]

Ligon TS, Fröhlich F, Chis OT, Banga JR, Balsa-Canto E, Hasenauer J.
GenSSI 2.0: multi-experiment structural identifiability analysis of SBML models.
Bioinformatics. 2018 Apr 15;34(8):1421-1423. doi: 10.1093/bioinformatics/btx735. [ABSTRACT]

Stapor P, Weindl D, Ballnus B, Hug S, Loos C, Fiedler A, Krause S, Hroß S, Fröhlich F, Hasenauer J, Wren J.
PESTO: Parameter EStimation TOolbox
Bioinformatics. 2018 Feb 15;34(4):705-707. doi: 10.1093/bioinformatics/btx676. [ABSTRACT]

2017

Bruderer R, Bernhardt OM, Gandhi T, Xuan Y, Sondermann J, Schmidt M, Gomez-Varela D, Reiter L.
Optimization of Experimental Parameters in Data-Independent Mass Spectrometry Significantly Increases Depth and Reproducibility of Results.
Mol Cell Proteomics 2017 Dec;16(12):2296-2309. doi: 10.1074/mcp.RA117.000314. Epub 2017 Oct 25. [ABSTRACT]

Ogilvie LA, Kovachev A, Wierling C., Lange BMH and Lehrach H.
Models of Models: A Translational Route for Cancer Treatment and Drug Development
Front. Oncol., 19 September 2017. doi: 10.3389/fonc.2017.00219. [ABSTRACT] 

Villaverde AF, Becker K, Banga JR.
PREMER: a Tool to Infer Biological Networks
IEEE/ACM Trans Comput Biol Bioinform. 2017 Oct 4. doi: 10.1109/TCBB.2017.2758786. [ABSTRACT]

Gábor A, Villaverde AF, Banga JR.
Parameter identifiability analysis and visualization in large-scale kinetic models of biosystems
BMC Syst Biol. 2017 May 5;11(1):54. doi: 10.1186/s12918-017-0428-y. [ABSTRACT]

2016

Villaverde AF, Barreiro A, Papachristodoulou A.
Structural Identifiability of Dynamic Systems Biology Models
PLoS Computational Biology 2016;12(10):e1005153 doi: 10.1371/journal.pcbi.1005153. [ABSTRACT]

Chis OT, Villaverde AF, Banga JR, Balsa-Canto E.
On the relationship between sloppiness and identifiability
Mathematical Biosciences 2016;282:147-161. doi: 10.1016/j.mbs.2016.10.009. Epub 2016 Oct 24 [ABSTRACT]

Villaverde AF, Becker K, Banga JR.
PREMER: Parallel Reverse Engineering of Biological Networks with Information Theory. In: Bartocci E., Lio P., Paoletti N. (eds)
Computational Methods in Systems Biology
CMSB 2016. Lecture Notes in Computer Science, vol 9859. Springer, Cham. [ABSTRACT]

Villaverde AF, Barreiro A, Papachristodoulou A.
Structural Identifiability Analysis via Extended Observability and Decomposition
IFAC-Papers On Line 2016;49(26): 171-177. doi: 10.1016/j.ifacol.2016.12.121. [ABSTRACT]