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Table 1 Key publications in apoptosis systems modeling

From: System-based approaches as prognostic tools for glioblastoma

Year Author Major findings Ref.
2000 Fussenegger et al. Theoretical study on mitochondrial permeabilization induced by BCL-2 family proteins [127]
2004 Eissing et al. Theoretical study analysing death receptor-induced apoptosis including bistability analysis [128]
2004 Bentele et al. ODE-based modelling of apoptosis signalling supported by quantitative Western blotting [125]
2005 Stucki et al. Theoretical study into mitochondrial cytochrome-c and SMAC release on caspase activation [129]
2006 Rehm et al. First study that combined single cell imaging and ODE modelling of caspase activation in response to mitochondrial permeabilization (MOMP) [47]
2006 Bagci et al. & Legewie et al. Theoretical studies that highlighted positive feedback loops which guarantee bistability subsequent to MOMP and co-operation in Apaf-1 oligomerisation [130, 131]
2007 Chen et al. Theoretical study on Bax-activation [132]
2007 Lavrik et al. Introduced robustness analysis into the field. Provided structural model of extrinsic apoptosis induced by CD95/Apo-1 [133]
2007 Eissing et al. Theoretical studies to evaluate robustness of computational models against parameter variations [134, 135]
2008 Albeck et al. Combined study employing live cell imaging of caspase activation and MOMP, flow cytometry, immunoblotting and modelling during death receptor-induced apoptosis [126]
2009 Zhang et al. Theoretical study into how genotoxic stress proceeds to MOMP and caspase activation [136]
2009 Chen et al. & Dussmann et al. Application of stochastic models based on cellular automata (CA) to study Bax activation in mitochondrial membranes during apoptosis [137, 138]
2009 & 2010 Rehm et al. & Huber et al. Spatial signal propagation during apoptosis signalling including experimental testing and mathematical modelling using partial differential equations (PDE) [123, 124]
2011 Aldridge et al. Combined in silico and wet-lab analyses focussed on TRAIL-induced apoptosis [139]
2011 Lau et al. Identification of spatial and temporal aspects of apoptosis signalling [140]
2012 Hector et al. Clinical application of caspase modelling to predict recurrence in CRC [13]
2012 Lee et al. Combined study employing mathematical modelling and wet-lab validation identifying optimal treatment scheduling for apoptosis re-sensitization [141]
2012 Gaudet et al. Comprehensive assessment with sensitivity analyses of the impact of cell-to-cell deviations in protein concentrations on apoptosis dynamics [142]
2012 Schleich et al. Combined theoretical and wet-lab analyses into the role of apoptosis activation by caspase-8 [143]
2013 Lindner et al. Use of BCL-2 systems analysis to predict patient response to chemotherapy in CRC [18]
2013 Murphy et al. Use of systems analysis to predict progression-free survival in GBM [17]
2014 Kallenberger et al. Combined in silico and wet-lab study into the regulation of apoptosis by caspase-8 [144]
2014 & 2015 Bertaux et al. & Roux et al. Theoretical study investigating fractional killing in apoptosis [145, 146]
2015 & 2016 Zhao et al. & Li et al. Theoretical study into the role played by mutations in apoptosis signalling [147, 148]
2017 Salvucci et al. Large scale validation of caspase modelling as independent prognostic biomarker in CRC and refinement of the prognostic power of apoptosis systems models with machine learning [19]
2017 Lindner et al. Large scale validation of BCL-2 modelling as independent prognostic biomarker in CRC and analysis of apoptosis systems models in molecular subtypes of CRC [20]
2018 Márquez-Jurado et al. Study combining mathematical modelling with experimental microscopy data focussed on the role played by mitochondria in regulating apoptosis [149]
2018 Hantusch et al. Regulation of BCL-XL via Bax retrotranslocation [150]