Research Publications

Preprints

1. Lakshmanan, L., Yee, Z., Gruber, J., Halliwell, B. and Gunawan, R. Thermodynamics analysis of mitochondrial DNA breakpoints reveals mechanistic details of deletion mutagenesis, bioRxiv (2018). external page abstract

2. Papili Gao, N., Hartmann, T. and Gunawan, R. CALISTA: Clustering and lineage inference in single-cell transcriptional analysis, bioRxiv (2018). external page abstract

Published

72. Noh, H., Shoemaker, J.E. and Gunawan, R. Network perturbation analysis of gene transcriptional profiles reveals protein targets and mechanism of action of drugs and influenza A viral infection, Nucleic Acids Research (2018). external page abstract

71. Perumal, T.M. and Gunawan, R. Elucidating cellular population dynamics by molecular density function perturbations, Processes, 6, 9 (2018). external page abstract (published in special issue on Biological Networks, and selected to be the cover page for February 2018 issue)

70. Papili-Gao, N., Ud-Dean, SMM., Gandrillon, O. and Gunawan, R. SINCERITIES: Inferring gene regulatory networks from time-stamped single cell transcriptional expression profiles. Bioinformatics 34, 258-266 (2018). external page abstract

69. Manesso, E., Srinath, S. and Gunawan, R. Multi-objective optimization of experiments using curvature and Fisher information matrix, 2017. Processes 5, 63 (2017). external page abstract (published in special issue on Biological Networks)

68. Kyriakopoulos, S., Ang, K.S., Lakshmanan, M., Huang, Z., Yoon, S., Gunawan, R. and Lee, D.Y. Kinetic modeling of mammalian cell culture bioprocessing: the quest to advance biomanufacturing. Biotechnology Journal (2017). external page abstract

67. Hutter, S., Villiger, T., Bruhlmann, D., Stettler, M., Broly, H., Soos, M. and Gunawan, R. Glycosylation Flux Analysis Reveals Dynamic Changes of Intracellular Glycosylation Flux Distribution In Chinese Hamster Ovary Fed-Batch Cultures. Metabolic Engineering 43, 9-20 (2017). external page abstract

66. Dual, J., Gerit, M., Hahn, P., Lakaemper, S., Leibacher, I., Lamprecht, A., Reichert, P., Vertti Quintero, N.S., Casadevall i Solvas, X., Gunawan, R. and deMello, A. Ultrasonic robotics in microfluidic cavities. J. Acoust. Soc. Am. 141, 3505 (2017). external page abstract

65. Gunawan, R. and Hutter, S. Assessing and Resolving Model Misspecifications in Metabolic Flux Analysis. Bioengineering 4,48 (2017). external page abstract

64. Liu, Y. and Gunawan, R. Bioprocess optimization under uncertainty using ensemble modeling. J. Biotechnology 244, 34-44 (2017). external page abstract

63. Richard, A., Boullu, L., Herbach, U., Bonnafoux, A., Morin, V., Vallin, E., Guillemin, A., Papili-Gao, N., Gunawan, R., Cosette, J., Arnaud, O., Kupiec, J., Espinasse, T., Gonin-Giraud, S. and Gandrillon, O. A surge in cell-to-cell molecular variability precedes the commitment in a differentiation process. PLoS Biology 14(12) (2016): e1002585. doi:10.1371/journal.pbio.1002585. external page abstract

62. Noh, H. and Gunawan, R. Inferring causal gene targets from time course expression data. IFAC-PapersOnLine 49(26), 350-356 (2016). external page abstract

61. Papili-Gao, N., Ud-Dean, SMM. and Gunawan, R. Gene regulatory network inference using time-stamped cross-sectional single cell expression data. IFAC-PapersOnLine 49(26), 147-152 (2016). external page abstract

60. Ud-Dean, SMM., Heise, S., Klamt, S. and Gunawan, R. TRaCE+: Ensemble inference of gene regulatory networks from transcriptional expression profiles of gene knock-out experiments. BMC Bioinformatics 17, 252 (2016). external page abstract

59. Noh, H. and Gunawan, R. Inferring gene targets of drugs and chemical compounds from gene expression profiles. Bioinformatics (2016). external page abstract

58. Ud-Dean, SMM. and Gunawan, R. Optimal design of gene knock-out experiments for gene regulatory network inference. Bioinformatics 32 (6): 875-883 (2016). external page abstract

57. Sriyudthsak, K., Uno, H., Gunawan, R. and Shiraishi, F. Using dynamic sensitivities to characterize metabolic reaction systems. Mathematical Biosciences (269) 153 - 163 (2015). external page abstract

56. Liu, Y., Manesso, E. and Gunawan, R. REDEMPTION: Reduced Dimension Ensemble Modeling and Parameter Estimation. Bioinformatics 31 (20): 3387-3389 (2015). external page abstract

55. Lakshmanan, LN., Gruber, J., Halliwell, B. and Gunawan, R. Are mutagenic non D-loop direct repeat motifs in mitochondrial DNA under a negative selection pressure?. Nucleic Acids Research 43(8): 4098-4108 (2015). external page abstract

54. Tam, Z., Gruber, J., Halliwell, B. and Gunawan R. Context-Dependent Role of Mitochondrial Fusion-Fission in Clonal Expansion of mtDNA Mutations. PLoS Computational Biology 11(5):e1004183 (2015). external page abstract

53. Liu, Y., and Gunawan, R. Parameter estimation of dynamic biological network models using integrated fluxes. BMC Systems Biology 8, 127 (2014). external page abstract

52. Ud-Dean, SMM., and Gunawan, R. Ensemble Inference and Inferability of Gene Regulatory Networks. PLoS ONE, 9(8), e103812 (2014). external page abstract

51. Siegenthaler, C., and Gunawan, R. Assessment of Network Inference Methods: How to Cope with an Underdetermined Problem. PLoS ONE, 9(3), e90481 (2014). external page abstract

50. Perumal, T. M., and Gunawan, R. pathPSA: a dynamical pathway-based parametric sensitivity analysis. Ind. Eng. Chem. Res., (2014). external page abstract

49. Tam, Z., Gruber, J., Ng, L.F., Halliwell, B. and Gunawan R. Effects of Lithium on Age-related Decline in Mitochondrial Turnover and Function in Caenorhabditis elegans. J Gerontol A, (2014). external page abstract

48. Tam, Z., Gruber, J., Halliwell, B. and Gunawan R. Mathematical Modeling of the Role of Mitochondrial Fusion and Fission in Mitochondrial DNA Maintenance. PLoS One, 8, e76230 (2013). external page abstract

47. Perumal, T. M., Krishna, S. M., Tallam, S. S. & Gunawan, R. Reduction of Kinetic Models using Dynamic Sensitivities. Computers & Chemical Engineering, 56, 37-45 (2013). external page abstract

46. Poovathingal, S. K., Gruber, J., Lakshmanan, LN., Halliwell, B. & Gunawan, R. Is mitochondrial DNA turnover slower than commonly assumed? Biogerontology 13, 557-564 (2012). external page abstract

45. Jia, G., Stephanopoulos, G., Gunawan, R. Incremental parameter estimation of kinetic metabolic network models. BMC Systems Biology 6, 142 (2012). external page abstract

44. Lakshmanan, LN., Gruber, J., Halliwell, B. & Gunawan, R. Role of direct repeat and stem-loop motifs in mtDNA deletions: cause or coincidence? PLoS One 7, e35271 (2012). external page abstract

43. Jia, G., Stephanopoulos, G. & Gunawan, R. Ensemble Kinetic Modeling of Metabolic Networks from Dynamic Metabolic Profiles. Metabolites 2, 891–912 (2012). external page abstract

42. Toldy, A.I., Badruddoza, A. Z. M., Lu, Z., Hatton, T. A., Gunawan, R., Rajagopalan, R. and Khan, S. A. Spherical Crystallization of Glycine from Monodisperse Microfluidic Emulsions. Crystal Growth & Design 12, 3977–3982 (2012). external page abstract

41. Poovathingal, S. K., Gruber, J., Ng, L. F., Halliwell, B. & Gunawan, R. Maximizing signal-to-noise ratio in the random mutation capture assay. Nucleic Acids Research 40, e35 (2012). external page abstract

40. G. Jia and R. Gunawan Construction of Kinetic Model Library of Metabolic Networks, In Proc. of the 8th IFAC International Symposium on Advanced Control of Chemical Process, pp. 952-957, 2012.

39. Jia, G., Stephanopoulos, G. N. & Gunawan, R. Parameter estimation of kinetic models from metabolic profiles : two-phase dynamic decoupling method. Bioinformatics 27, 1964–1970 (2011). external page abstract

38. Perumal, T. M. & Gunawan, R. Understanding dynamics using sensitivity analysis: caveat and solution. BMC Systems Biology 5, 41 (2011). external page abstract

37. T.M. Perumal and R. Gunawan. Impulse parametric sensitivity analysis. In Proc. of the 18th IFAC World Congress, pp. 9896-9890, 2011.

36. G. Jia and R. Gunawan, Construction of Kinetic Model Library of Metabolic Networks from Dynamic Profiles, In the 8th International Workshop on Computational Systems Biology, TICSP series #57, 2011.

35. Z. Y. Tam and R. Gunawan, On the Roles of Mitochondrial Fusion-Fission in Mitochondrial Genome Integrity, In Proc of the 8th International Workshop on Computational System Biology, TICSP series #57, 2011.

34. Tam, Z. Y., Cai, Y. H. & Gunawan, R. Elucidating cytochrome C release from mitochondria: insights from an in silico three-dimensional model. Biophysical Journal 99, 3155–63 (2010). external page abstract

33. Srinath, S. & Gunawan, R. Parameter identifiability of power-law biochemical system models. Journal of Biotechnology 149, 132–40 (2010). external page abstract

32. Poovathingal, S. K. & Gunawan, R. Global parameter estimation methods for stochastic biochemical systems. BMC Bioinformatics 11, 414 (2010). external page abstract

31. Gruber, J., Poovathingal, S. K., Fang, N. L., Gunawan R. and B. Halliwell. Caenorhabditis elegans life span studies: the challenge of maintaining synchronous cohorts. Rejuvenation Research 13, 347–9 (2010). external page abstract

30. Poovathingal, S. K., Gruber, J., Halliwell, B. & Gunawan, R. Stochastic drift in mitochondrial DNA point mutations: a novel perspective ex silico. PLoS Computational Biology 5, e1000572 (2009). external page abstract

29. Perumal, T.M., Wu, Y. & Gunawan, R. Dynamical analysis of cellular networks based on the Green’s function matrix. Journal of Theoretical Biology 261, 248–59 (2009). external page abstract

28. S.R. Taylor, R. Gunawan, L. R. P. and F. J. D. I. Sensitivity measures for oscillating systems: application to mammalian circadian gene network. IEEE Transactions on Automatic Control 53, 177–188 (2009). external page abstract

27. Gunawan, R., Fusman, I. & Braatz, R. D. Parallel High-Resolution Finite Volume Simulation of Particulate Processes. AIChE J. 54, 1449–1458 (2008). external page abstract

26. T.M. Perumal, Y. Wu, and R. Gunawan. Robustness analysis of cellular systems for in silico drug discovery. In Proc. of the 17th IFAC World Congress, pp. 1607-12612, 2008. external page abstract

25. Gunawan, R. & Doyle, F. J. Phase sensitivity analysis of circadian rhythm entrainment. Journal of Biological Rhythms 22, 180–94 (2007). external page abstract

24. Gunawan, R. & Doyle, F. J. Isochron-based phase response analysis of circadian rhythms. Biophysical Journal 91, 2131–41 (2006). external page abstract

23. Doyle, F. J., Gunawan, R., Bagheri, N., Mirsky, H. & To, T. L. Circadian rhythm: A natural, robust, multi-scale control system. Computers & Chemical Engineering 30, 1700–1711 (2006). external page abstract

22. Braatz, R. D., Alkire, R. C., Seebauer, E. G., Drews, T. O., Rusli, E., Karulkar, M., Xue, F., Qin, Y., Jung M. Y. L. and Gunawan R. A multiscale systems approach to microelectronic processes. Computers & Chemical Engineering 30, 1643–1656 (2006). external page abstract

21. Braatz, R. D., Alkire, R. C., Seebauer, E. G., Rusli, E., Gunawan, R., Drews, T. O., Li, X. and He Y. Perspectives on the design and control of multiscale systems. Journal of Process Control 16, 193–204 (2006). external page abstract

20. F. J. Doyle III, R. Gunawan, N. Bagheri, H. Mirsky, and T.-L. To. Circadian rhythm: A natural, robust, multi-scale control system. In Proc. of Chem. Process Control, Alberta, Canada, January 2006. external page abstract

19. Gunawan, R., Cao, Y., Petzold, L. & Doyle, F. J. Sensitivity analysis of discrete stochastic systems. Biophysical Journal 88, 2530–40 (2005). external page abstract

18. Gadkar, K. G., Gunawan, R. & Doyle, F. J. Iterative approach to model identification of biological networks. BMC Bioinformatics 6, 155 (2005). external page abstract

17. R. Gunawan and F. J. Doyle III. Phase sensitivity analysis of a circadian gene network. In Proc. of the 44^th IEEE Conf. on Decision & Control and European Control Conf., December 2005.

16. Jung, M. Y. L., Gunawan, R., Braatz, R. D. & Seebauer, E. G. Pair diffusion and kick-out: Contributions to diffusion of boron in silicon. AIChE Journal 50, 3248–3256 (2004). external page abstract

15. Jung, M. Y. L., Gunawan, R., Braatz, R. D. & Seebauer, E. G. A Simplified Picture for Transient Enhanced Diffusion of Boron in Silicon. Journal of The Electrochemical Society 151, G1 (2004). external page abstract

14. Jung, M. Y. L., Gunawan, R., Braatz, R. D. & Seebauer, E. G. Effect of near-surface band bending on dopant profiles in ion-implanted silicon. Journal of Applied Physics 95, 1134 (2004). external page abstract

13. Gunawan, R., Fusman, I. & Braatz, R. D. High resolution algorithms for multidimensional population balance equations. AIChE Journal 50, 2738–2749 (2004). external page abstract

12. Gunawan, R., Jung, M. Y. L., Seebauer, E. G. & Braatz, R. D. Optimal control of rapid thermal annealing in a semiconductor process. Journal of Process Control 14, 423–430 (2004). external page abstract

11. Jung, M. Y. L., Gunawan, R., Braatz, R. D. & Seebauer, E. G. Ramp-Rate Effects on Transient Enhanced Diffusion and Dopant Activation. Journal of The Electrochemical Society 150, G838 (2003). external page abstract

10. Gunawan, R., Jung, M. Y. L., Braatz, R. D. & Seebauer, E. G. Parameter Sensitivity Analysis Applied to Modeling Transient Enhanced Diffusion and Activation of Boron in Silicon. Journal of The Electrochemical Society 150, G758 (2003). external page abstract

9. Gunawan, R., Jung, M. Y. L., Seebauer, E. G. & Braatz, R. D. Maximum A Posteriori Estimation of Transient Enhanced Diffusion Energetics. AIChE Journal 49, (2003). external page abstract

8. Dev, K., Jung, M., Gunawan, R., Braatz, R. & Seebauer, E G.. Mechanism for coupling between properties of interfaces and bulk semiconductors. Physical Review B 68, 195311 (2003). external page abstract

7. Gunawan, R., Jung, M. Y. L., Seebauer, E. G. and Braatz, R. D. Optimal control of transient enhanced diffusion. In Proc. of the IFAC Symp. on Advanced Control of Chemical Processes, pp. 603-608, 2003.

6. Gunawan, R., Ma, D. L., Fujiwara, M. and Braatz, R. D. Identification of Kinetic Parameters in Multidimensional Crystallization Processes. International Journal of Modern Physics B 16, 367–374 (2002). external page abstract

5. Fujiwara, M., Pirkle Jr., J. C., Togkalidou, T., Ma, D. L., Gunawan, R. and Braatz, R. D. A holistic approach to materials process design. J. Materials Edu. 24, 65–70 (2002).

4. Gunawan, R., Jung, M. Y. L., Braatz, R. D. and Seebauer E. G. Systems analysis applied to modeling dopant activation and TED in rapid thermal annealing. In Proc. of the 10th IEEE Intl. Conf. on Advanced Thermal Processing of Semiconductors, pp. 107-110, 2002.

3. Gunawan, R., Russell, E. L. & Braatz, R. D. Comparison of theoretical and computational characteristics of dimensionality reduction methods for large-scale uncertain systems. Journal of Process Control 11, 543–552 (2001). external page abstract

2. Gunawan, R., Russell E. L. and Braatz, R. D. Robustness analysis of multivariable systems with time delays. In Proc. of European Control Conf., pp. 1882-1887, 2001.

1. Jung, M. Y. L., Gunawan, R., Braatz, R. D. and Seebauer E. G. New physics for modeling transient enhanced diffusion in RTP. In Rapid Thermal & Other Short-Time Processing Technologies, vol. 2000-9, pp. 15-20, 2000.