Executable cell biology

By Jasmin Fisher, Thomas A. Henzinger. Nature Biotechnology, 2007

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The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

Efficient modeling, simulation and coarse-graining of biological complexity with NFsim (2011, methodology): “Computational methods offer the promise of transforming quantitative experimental data into predictive and testable models of cellular behavio”
Structure-based Systems Biology for Analyzing Off-target Binding (2011, background): “Continued progress in generating, mining and integrating omics-data [120– 125], the active development of algorithms for network biology [126–128], and the emergence of executable biology [129,130] will provide rich resources and computational frameworks to address the network reconstruction issue.”
Computational thinking and thinking about computing (2008, methodology): “Computational thinking is transforming biology, ﬁrst with the shotgun sequencing algorithm accelerating our ability to sequence the human genome, and now with our abstractions representing dynamic processes found in nature, from the cell cycle to protein folding (e.g. Fisher & Henzinger 2007).”
Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction (2009, methodology): “Boolean modelling has previously been applied to biological regulatory and signalling networks (Kauffman, 1969; Thomas and D’Ari, 1990; Huang and Ingber, 2000; Thomas and Kaufman, 2001; de Jong, 2002; Chaves et al, 2005; Fauré et al, 2006; Fisher and Henzinger, 2007; Gupta et al, 2007; Saez-Rodrigue”