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- The Systems Biology Graphical Notation.
- The Transcriptional Landscape of the Mammalian Genome, The FANTOM3 Consortium, Science, 2 September 2006
- Systems-Level Dissection of the Cell-Cycle Oscillator: Bypassing Positive Feedback Produces Damped Oscillations, Pomerening, et al., Cell, 26 August 2006
- Exploring the regulation of human neural precursor cell differentiation using arrays of signaling microenvironments, Molecular Systems Biology, July 2006
- Evolutionary and Physiological Importance of Hub Proteins, PLoS Computational Biology
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