Natasa Miskov-Zivanov
ABSTRACT
Although there have been several recent attempts to automate steps of the process of model development and analysis in cell signaling networks, closing the overall cycle between information extraction, model assembly and analysis, and design of questions to guide new information search and experiments still requires a significant amount of human intervention. In this paper, we give an overview of challenges in this process, and outline our approaches to tackle these challenges.
- N. Miskov-Zivanov, D. Marculescu, and J. R. Faeder, "Dynamic behavior of cell signaling networks: model design and analysis automation." in Proc. of Design Automation Conference (DAC), Article 8, 6 p., June 2013. Google Scholar
Digital Library
- N. Miskov-Zivanov, P. Wei, C.S.C. Loh, "THiMED: Time in Hierarchical Model Extraction and Design," in Proc. of Computational Methods in Systems Biology (CMSB), pp. 260--263, November 2014.Google Scholar
- A. Garg, K. Mohanram, A. Di Cara, G. De Micheli, and I. Xenarios, "Modeling stochasticity and robustness in gene regulatory networks," Bioinformatics, vol. 25, pp. i101-i109, 2009. Google ScholarDigital Library
- N. Miskov-Zivanov, M. S. Turner, L. P. Kane, P. A. Morel, and J. R. Faeder, "The duration of T cell stimulation is a critical determinant of cell fate and plasticity," in Science Signaling, 6, ra97, November 2013.Google Scholar
- N. Miskov-Zivanov, P. Zuliani, E. M. Clarke, and J. R. Faeder, "Studies of biological networks with statistical model checking: application to immune system cells," in Proc. of ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM-BCB), September 2013, pp. 728. Google ScholarDigital Library
- N. Miskov-Zivanov, A. Bresticker, S. Venkatakrishnan, P. Kashinkunti, D. Krishnaswamy, D. Marculescu and J. R. Faeder, "Regulatory Network Analysis Acceleration with Reconfigurable Hardware," in Proc. of International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), pp. 149--152, September 2011.Google Scholar
- N. Miskov-Zivanov, A. Bresticker, D. Krishnaswamy, S. Venkatakrishnan, D. Marculescu and J. R. Faeder, "Emulation of Biological Networks in Reconfigurable Hardware," in Proc. of ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM-BCB), pp. 536--540, August 2011. Google ScholarDigital Library
Index Terms
- Automation of Biological Model Learning, Design and Analysis
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