Bioinformatics (Thomas Dandekar, Meik Kunz)

Breitenbach T, Liang C, Beyersdorf N et al (2019a) Analyzing pharmacological intervention points:

a method to calculate external stimuli to switch between steady states in regulatory networks.

PLoS Comput Biol 15(7):e1007075. https://doi.org/10.1371/journal.pcbi.1007075

Breitenbach T, Lorenz K, Dandekar T (2019b) How to steer and control ERK and the ERK signaling

cascade exemplified by looking at cardiac insufficiency. Int J Mol Sci 20(9):2179. https://doi.

org/10.3390/ijms20092179

Brietz A, Schuch KV, Wangorsch G et al (2016) Analyzing ERK 1/2 signalling and targets. Mol

BioSyst 12(8):2436–2446. https://doi.org/10.1039/c6mb00255b

Göttlich C, Müller LC, Kunz M et al (2016) A combined 3D tissue engineered in vitro/in silico lung

tumor model for predicting drug effectiveness in specific mutational backgrounds. J Vis Exp

110:e53885. https://doi.org/10.3791/53885 (*Cancer is modeled here both in vitro and in silico,

the two complementing each other)

Karl S, Dandekar T (2013) Jimena: efficient computing and system state identification for genetic

regulatory networks. BMC Bioinformatics 14:306. https://doi.org/10.1186/1471-2105-14-306

(*Explains analysis with Jimena software, useful for all systems biology modeling)

Klipp E, Liebermeister W, Wierling C et al (2016) Edda klipp systems biology: a textbook, 2nd edn.

isbn: 978-3-527-33636-4

Kunz M, Dandekar T, Naseem M (2017) A systems biology methodology combining transcriptome

and interactome datasets to assess the implications of cytokinin signaling for plant immune net

works. Methods Mol Biol 1569:165–173. https://doi.org/10.1007/978-1-4939-6831-2_14

Kunz M, Jeromin J, Fuchs M et al (2020) In silico signaling modeling to understand cancer pathways

and treatment responses. Brief Bioinform 21(3):1115–1117. https://doi.org/10.1093/bib/bbz033

Naseem M, Philippi N, Hussain A et al. (2012) Integrated systems view on networking by hormones

in Arabidopsis immunity reveals multiple crosstalk for cytokinin. Plant Cell 24(5):1793–1814.

https://doi.org/10.1105/tpc.112.098335 (*This work shows how experiment and modeling in

bioinformatics work together to elucidate a complex plant hormone network here)

5 Systems Biology Helps to Discover Causes of Disease