Gunawan:Publications

Chemical and Biological Systems Engineering Laboratory

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Book Chapter

• R. Gunawan, K. Gadkar, and F. J. Doyle III. Methods to identify cellular architecture and dynamics from experimental data. In Z. Szallasi, V. Periwal, and J. Stelling (Eds.), System Modeling in Cellular Biology, MIT Press, 2006.
• J. Shoemaker, R. Gunawan, and F. J. Doyle III. Model-based Optimal Experimental Design in Biological Systems. In J. Varner (Eds.), Methods in Molecular Biology: Caspases, to be published by Humana Press, 2006. in preparation
• S. Hildebrandt, N. Bagheri, R. Gunawan, H. Mirsky, J. Shoemaker, S. Taylor, and F. J. Doyle III. Systems Analysis of Biological Networks in Systems Biology, to be published by Academic Press, 2006.

Journal Articles

1. Tam ZY, Cai YH, and Gunawan R. Elucidating cytochrome C release from mitochondria: insights from an in silico three-dimensional model. Biophys J. 2010 Nov 17;99(10):3155-63. DOI:10.1016/j.bpj.2010.09.041 |
2. Poovathingal SK and Gunawan R. Global parameter estimation methods for stochastic biochemical systems. BMC Bioinformatics. 2010 Aug 6;11:414. DOI:10.1186/1471-2105-11-414 |
3. Srinath S and Gunawan R. Parameter identifiability of power-law biochemical system models. J Biotechnol. 2010 Sep 1;149(3):132-40. DOI:10.1016/j.jbiotec.2010.02.019 |
4. Poovathingal SK, Gruber J, Halliwell B, and Gunawan R. Stochastic drift in mitochondrial DNA point mutations: a novel perspective ex silico. PLoS Comput Biol. 2009 Nov;5(11):e1000572. DOI:10.1371/journal.pcbi.1000572 |
5. Perumal TM, Wu Y, and Gunawan R. Dynamical analysis of cellular networks based on the Green's function matrix. J Theor Biol. 2009 Nov 21;261(2):248-59. DOI:10.1016/j.jtbi.2009.07.037 |
6. Gunawan R and Doyle FJ 3rd. Phase sensitivity analysis of circadian rhythm entrainment. J Biol Rhythms. 2007 Apr;22(2):180-94. DOI:10.1177/0748730407299194 |
7. Gunawan R and Doyle FJ 3rd. Isochron-based phase response analysis of circadian rhythms. Biophys J. 2006 Sep 15;91(6):2131-41. DOI:10.1529/biophysj.105.078006 |
8. Gadkar KG, Gunawan R, and Doyle FJ 3rd. Iterative approach to model identification of biological networks. BMC Bioinformatics. 2005 Jun 20;6:155. DOI:10.1186/1471-2105-6-155 |
9. Gunawan R, Cao Y, Petzold L, and Doyle FJ 3rd. Sensitivity analysis of discrete stochastic systems. Biophys J. 2005 Apr;88(4):2530-40. DOI:10.1529/biophysj.104.053405 |

Peer reviewed Conference Proceedings

• Suresh P, Gruber J, Halliwell B, and Gunawan R. (2010) Sarcopenia in silico, In AiChe annual general meeting, Salt Lake City, USA, Nov 7-12.

• Suresh P, Gruber J, Halliwell B, Gunawan R. (2010) Elucidating Mechanisms of Age-dependent Accumulation of Mitochondrial DNA Deletions – An in silico Approach, In Gordon Research Conference on Biology of Aging, Switzerland, Aug 22-27. (poster).

• Srinath S , Gunawan R. (2010) Parameter Identifiability of Metabolic Network Models, In Satellite Conference of the International Congress of Mathematics, Hyderabad, India, Aug 16-18

• Perumal TM , Gunawan R. (2010) In analyzing the complex dynamics of biochemical pathways, In Satellite Conference of the International Congress of Mathematics, Hyderabad, India, Aug 16-18

• Srinath S , Yuan Z, Gunawan R. (2010) Identifiability Analysis of Decoupled Power-Law Models, In 5th International Symposium on Design, Operation and Control of Chemical Processes (PSE Asia), Singapore, July 25-28

• Gengjie J , Gunawan R. (2010) Parameter Estimation of Kinetic Models from Incomplete Metabolic Profiles, In 5th International Symposium on Design, Operation and Control of Chemical Processes (PSE Asia), Singapore, July 25-28

• Srinath S , Gunawan R. (2010) Parameter Identifiability in Kinetic Modeling of Metabolic Pathways, In Metabolic Engineering Conference VIII, Jeju Island, South Korea, Jun 13 - 17 (poster)

• Perumal TM , Gunawan R. (2009) Information transfer in Biological Network Motifs, In 10th International Conference on Systems Biology (ICSB), Stanford, California, USA, Aug 30 - Sep 4 (poster)

• Suresh P , Gruber J, Halliwell B, Gunawan R. (2009) Stochasticity in mitochondrial DNA point mutation and its relevance in Caenorhabditis elegans Aging, In 10th International Conference on Systems Biology (ICSB), Stanford, California, USA, Aug 30 - Sep 4 (poster)

• Perumal TM , Gunawan R. (2009) Information-theoretic global robustness analysis of cellular systems: A molecular perturbation approach, In Third International Conference on Foundations of Systems Biology in Engineering (FOSBE), Denver, Colorado, USA, August 9 - 12, PP: 52 - 55 (poster)

• Suresh P , Gruber J, Halliwell B, Gunawan R. (2009) A global approach for estimating the kinetic parameters of stochastic biological systems, In Third International Conference on Foundations of Systems Biology in Engineering (FOSBE), Denver, Colorado, USA, August 9 - 12, PP: 56 - 59 (poster)

• Srinath S, Gunawan R . (2009) Identifiability Analysis of Metabolic Networks, In 11th International Conference on Molecular Systems Biology (ICMSB), Shanghai, China, June 21-25

• Suresh P, Gruber J, Halliwell B, Gunawan R . (2008) Aging Studies: A Stochastic Approach in point mutation dynamics in mouse model In AiChe annual general meeting , Philadelphia, USA, Nov 16-21

• Perumal TM, Yan W, Gunawan R . (2008) Robustness Analysis of Cellular Systems for In Silico Drug Discovery, In 17th World Congress - The International Federation of Automatic Control (IFAC), Seoul, Korea, July 6-11, PP: 12607-12612

• Perumal TM , Yan W, Gunawan R. (2008) In Silico Dynamical Analysis of Cellular Systems: A Molecular Perturbation Approach, In 12th Annual International Conference on Research in Computational Molecular Biology (RECOMB), Singapore, March 30 - April 2 (poster)

• Suresh P , Gruber J, Halliwell B, Gunawan R. (2008) Aging Studies: A Stochastic Approach, In 12th Annual International Conference on Research in Computational Molecular Biology (RECOMB), Singapore, March 30 - April 2 (poster)

• Perumal TM, Yan W, Gunawan R . (2008) In Silico Molecular Analysis: Application to Fas-Induced Apoptotic Pathway, In 10th International Conference on Molecular Systems Biology (ICMSB), Manila, Philippines, February 25-28 (poster)

• Perumal TM, Yan W, Gunawan R . (2007) In Silico Molecular Analysis: Application to the Fas-induced Apoptotic Pathway, In 8th International Conference on Systems Biology (ICSB), California, USA, October 1-6 (poster)