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 pageabstractcall_made
2. Papili Gao, N., Hartmann, T. and Gunawan, R. CALISTA: Clustering and lineage inference in single-cell transcriptional analysis, bioRxiv (2018). external pageabstractcall_made
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 pageabstractcall_made
71. Perumal, T.M. and Gunawan, R. Elucidating cellular population dynamics by molecular density function perturbations, Processes, 6, 9 (2018). external pageabstractcall_made (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 pageabstractcall_made
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 pageabstractcall_made (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 pageabstractcall_made
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 pageabstractcall_made
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 pageabstractcall_made
65. Gunawan, R. and Hutter, S. Assessing and Resolving Model Misspecifications in Metabolic Flux Analysis. Bioengineering 4,48 (2017). external pageabstractcall_made
64. Liu, Y. and Gunawan, R. Bioprocess optimization under uncertainty using ensemble modeling. J. Biotechnology 244, 34-44 (2017). external pageabstractcall_made
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 pageabstractcall_made
62. Noh, H. and Gunawan, R. Inferring causal gene targets from time course expression data. IFAC-PapersOnLine 49(26), 350-356 (2016). external pageabstractcall_made
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 pageabstractcall_made
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 pageabstractcall_made
59. Noh, H. and Gunawan, R. Inferring gene targets of drugs and chemical compounds from gene expression profiles. Bioinformatics (2016). external pageabstractcall_made
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 pageabstractcall_made
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 pageabstractcall_made
56. Liu, Y., Manesso, E. and Gunawan, R. REDEMPTION: Reduced Dimension Ensemble Modeling and Parameter Estimation. Bioinformatics 31 (20): 3387-3389 (2015). external pageabstractcall_made
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 pageabstractcall_made
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 pageabstractcall_made
53. Liu, Y., and Gunawan, R. Parameter estimation of dynamic biological network models using integrated fluxes. BMC Systems Biology 8, 127 (2014). external pageabstractcall_made
52. Ud-Dean, SMM., and Gunawan, R. Ensemble Inference and Inferability of Gene Regulatory Networks. PLoS ONE, 9(8), e103812 (2014). external pageabstractcall_made
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 pageabstractcall_made
50. Perumal, T. M., and Gunawan, R. pathPSA: a dynamical pathway-based parametric sensitivity analysis. Ind. Eng. Chem. Res., (2014). external pageabstractcall_made
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 pageabstractcall_made
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 pageabstractcall_made
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 pageabstractcall_made
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 pageabstractcall_made
45. Jia, G., Stephanopoulos, G., Gunawan, R. Incremental parameter estimation of kinetic metabolic network models. BMC Systems Biology 6, 142 (2012). external pageabstractcall_made
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 pageabstractcall_made
43. Jia, G., Stephanopoulos, G. & Gunawan, R. Ensemble Kinetic Modeling of Metabolic Networks from Dynamic Metabolic Profiles. Metabolites 2, 891–912 (2012). external pageabstractcall_made
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 pageabstractcall_made
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 pageabstractcall_made
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 pageabstractcall_made
38. Perumal, T. M. & Gunawan, R. Understanding dynamics using sensitivity analysis: caveat and solution. BMC Systems Biology 5, 41 (2011). external pageabstractcall_made
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 pageabstractcall_made
33. Srinath, S. & Gunawan, R. Parameter identifiability of power-law biochemical system models. Journal of Biotechnology 149, 132–40 (2010). external pageabstractcall_made
32. Poovathingal, S. K. & Gunawan, R. Global parameter estimation methods for stochastic biochemical systems. BMC Bioinformatics 11, 414 (2010). external pageabstractcall_made
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 pageabstractcall_made
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 pageabstractcall_made
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 pageabstractcall_made
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 pageabstractcall_made
27. Gunawan, R., Fusman, I. & Braatz, R. D. Parallel High-Resolution Finite Volume Simulation of Particulate Processes. AIChE J. 54, 1449–1458 (2008). external pageabstractcall_made
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 pageabstractcall_made
25. Gunawan, R. & Doyle, F. J. Phase sensitivity analysis of circadian rhythm entrainment. Journal of Biological Rhythms 22, 180–94 (2007). external pageabstractcall_made
24. Gunawan, R. & Doyle, F. J. Isochron-based phase response analysis of circadian rhythms. Biophysical Journal 91, 2131–41 (2006). external pageabstractcall_made
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 pageabstractcall_made
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 pageabstractcall_made
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 pageabstractcall_made
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 pageabstractcall_made
19. Gunawan, R., Cao, Y., Petzold, L. & Doyle, F. J. Sensitivity analysis of discrete stochastic systems. Biophysical Journal 88, 2530–40 (2005). external pageabstractcall_made
18. Gadkar, K. G., Gunawan, R. & Doyle, F. J. Iterative approach to model identification of biological networks. BMC Bioinformatics 6, 155 (2005). external pageabstractcall_made
17. R. Gunawan and F. J. Doyle III. Phase sensitivity analysis of a circadian gene network. In Proc. of the 44th 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 pageabstractcall_made
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 pageabstractcall_made
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 pageabstractcall_made
13. Gunawan, R., Fusman, I. & Braatz, R. D. High resolution algorithms for multidimensional population balance equations. AIChE Journal 50, 2738–2749 (2004). external pageabstractcall_made
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 pageabstractcall_made
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 pageabstractcall_made
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 pageabstractcall_made
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 pageabstractcall_made
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 pageabstractcall_made
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 pageabstractcall_made
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 pageabstractcall_made
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.