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Rudiyanto Gunawan, Ph.D. - Publications

Affiliations: 
2006-2010 Department of Chemical and Biomolecular Engineering National University of Singapore, Singapore, Singapore 
 2011-2018 Institute for Chemical and Bioengineering Eidgenössische Technische Hochschule Zürich, Zürich, ZH, Switzerland 
 2018- Department of Chemical and Biological Engineering State University of New York, Buffalo, Buffalo, NY, United States 
Area:
Chemical Engineering
Website:
http://www.cabselab.com
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72 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Chrysinas P, Venkatesan S, Ang I, Ghosh V, Chen C, Neelamegham S, Gunawan R. Cell and tissue-specific glycosylation pathways informed by single-cell transcriptomics. Biorxiv : the Preprint Server For Biology. PMID 38260527 DOI: 10.1101/2023.09.26.559616  0.75
2022 Odunsi K, Qian F, Lugade AA, Yu H, Geller MA, Fling SP, Kaiser JC, Lacroix AM, D'Amico L, Ramchurren N, Morishima C, Disis ML, Dennis L, Danaher P, Warren S, ... ... Gunawan R, et al. Metabolic adaptation of ovarian tumors in patients treated with an IDO1 inhibitor constrains antitumor immune responses. Science Translational Medicine. 14: eabg8402. PMID 35294258 DOI: 10.1126/scitranslmed.abg8402  0.75
2021 Meamardoost S, Bhattacharya M, Hwang EJ, Komiyama T, Mewes C, Wang L, Zhang Y, Gunawan R. FARCI: Fast and Robust Connectome Inference. Brain Sciences. 11. PMID 34942857 DOI: 10.3390/brainsci11121556  0.759
2021 Ravi S, Gunawan R. ΔFBA-Predicting metabolic flux alterations using genome-scale metabolic models and differential transcriptomic data. Plos Computational Biology. 17: e1009589. PMID 34758020 DOI: 10.1371/journal.pcbi.1009589  0.777
2021 Noh H, Hua Z, Chrysinas P, Shoemaker JE, Gunawan R. DeltaNeTS+: elucidating the mechanism of drugs and diseases using gene expression and transcriptional regulatory networks. Bmc Bioinformatics. 22: 108. PMID 33663384 DOI: 10.1186/s12859-021-04046-2  0.723
2019 Teo E, Ravi S, Barardo D, Kim HS, Fong S, Cazenave-Gassiot A, Tan TY, Ching J, Kovalik JP, Wenk MR, Gunawan R, Moore PK, Halliwell B, Tolwinski N, Gruber J. Metabolic stress is a primary pathogenic event in transgenic expressing pan-neuronal human amyloid beta. Elife. 8. PMID 31610847 DOI: 10.7554/Elife.50069  0.771
2018 Noh H, Shoemaker JE, 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. PMID 29325153 DOI: 10.1093/Nar/Gkx1314  0.768
2017 Kyriakopoulos S, Ang KS, Lakshmanan M, Huang Z, Yoon S, Gunawan R, Lee DY. Kinetic modeling of mammalian cell culture bioprocessing: the quest to advance biomanufacturing. Biotechnology Journal. PMID 29027766 DOI: 10.1002/Biot.201700229  0.354
2017 Papili Gao N, Ud-Dean SMM, Gandrillon O, Gunawan R. SINCERITIES: Inferring gene regulatory networks from time-stamped single cell transcriptional expression profiles. Bioinformatics (Oxford, England). PMID 28968704 DOI: 10.1093/Bioinformatics/Btx575  0.336
2017 Gunawan R, Hutter S. Assessing and Resolving Model Misspecifications in Metabolic Flux Analysis. Bioengineering (Basel, Switzerland). 4. PMID 28952528 DOI: 10.3390/Bioengineering4020048  0.756
2017 Hutter S, Villiger TK, Brühlmann D, Stettlerc M, Broly H, Soos M, Gunawan R. Glycosylation flux analysis reveals dynamic changes of intracellular glycosylation flux distribution in Chinese hamster ovary fed-batch cultures. Metabolic Engineering. PMID 28754360 DOI: 10.1016/J.Ymben.2017.07.005  0.755
2017 Liu Y, Gunawan R. Bioprocess optimization under uncertainty using ensemble modeling. Journal of Biotechnology. PMID 28137617 DOI: 10.1016/J.Jbiotec.2017.01.013  0.345
2016 Richard A, Boullu L, Herbach U, Bonnafoux A, Morin V, Vallin E, Guillemin A, Papili Gao N, Gunawan R, Cosette J, Arnaud O, Kupiec JJ, Espinasse T, Gonin-Giraud S, Gandrillon O. Single-Cell-Based Analysis Highlights a Surge in Cell-to-Cell Molecular Variability Preceding Irreversible Commitment in a Differentiation Process. Plos Biology. 14: e1002585. PMID 28027290 DOI: 10.1371/Journal.Pbio.1002585  0.33
2016 Ud-Dean SM, Heise S, Klamt S, Gunawan R. TRaCE+: Ensemble inference of gene regulatory networks from transcriptional expression profiles of gene knock-out experiments. Bmc Bioinformatics. 17: 252. PMID 27342648 DOI: 10.1186/S12859-016-1137-Z  0.31
2016 Noh H, Gunawan R. Inferring gene targets of drugs and chemical compounds from gene expression profiles. Bioinformatics (Oxford, England). PMID 27153589 DOI: 10.1093/Bioinformatics/Btw148  0.776
2016 Noh H, Ziyi H, Gunawan R. Inferring Causal Gene Targets from Time Course Expression Data Ifac-Papersonline. 49: 350-356. DOI: 10.1016/J.Ifacol.2016.12.151  0.339
2016 Gao NP, Minhaz Ud-Dean S, Gunawan R. Gene Regulatory Network Inference Using Time-Stamped Cross-Sectional Single Cell Expression Data Ifac-Papersonline. 49: 147-152. DOI: 10.1016/J.Ifacol.2016.12.117  0.319
2015 Ud-Dean SM, Gunawan R. Optimal design of gene knockout experiments for gene regulatory network inference. Bioinformatics (Oxford, England). PMID 26568633 DOI: 10.1093/Bioinformatics/Btv672  0.324
2015 Sriyudthsak K, Uno H, Gunawan R, Shiraishi F. Using dynamic sensitivities to characterize metabolic reaction systems. Mathematical Biosciences. 269: 153-63. PMID 26384553 DOI: 10.1016/J.Mbs.2015.09.002  0.33
2015 Liu Y, Manesso E, Gunawan R. REDEMPTION: reduced dimension ensemble modeling and parameter estimation. Bioinformatics (Oxford, England). 31: 3387-9. PMID 26076722 DOI: 10.1093/Bioinformatics/Btv365  0.332
2015 Tam ZY, Gruber J, Halliwell B, Gunawan R. Context-Dependent Role of Mitochondrial Fusion-Fission in Clonal Expansion of mtDNA Mutations. Plos Computational Biology. 11: e1004183. PMID 25996936 DOI: 10.1371/Journal.Pcbi.1004183  0.786
2014 Liu Y, Gunawan R. Parameter estimation of dynamic biological network models using integrated fluxes. Bmc Systems Biology. 8: 127. PMID 25403239 DOI: 10.1186/S12918-014-0127-X  0.326
2014 Ud-Dean SM, Gunawan R. Ensemble inference and inferability of gene regulatory networks. Plos One. 9: e103812. PMID 25093509 DOI: 10.1371/Journal.Pone.0103812  0.324
2014 Tam ZY, Gruber J, Ng LF, Halliwell B, Gunawan R. Effects of lithium on age-related decline in mitochondrial turnover and function in Caenorhabditis elegans. The Journals of Gerontology. Series a, Biological Sciences and Medical Sciences. 69: 810-20. PMID 24398558 DOI: 10.1093/Gerona/Glt210  0.779
2014 Perumal TM, Gunawan R. PathPSA: A dynamical pathway-based parametric sensitivity analysis Industrial and Engineering Chemistry Research. 53: 9149-9157. DOI: 10.1021/Ie403277D  0.338
2013 Tam ZY, Gruber J, Halliwell B, Gunawan R. Mathematical modeling of the role of mitochondrial fusion and fission in mitochondrial DNA maintenance. Plos One. 8: e76230. PMID 24146842 DOI: 10.1371/Journal.Pone.0076230  0.782
2013 Perumal TM, Madgula Krishna S, Tallam SS, Gunawan R. Reduction of kinetic models using dynamic sensitivities Computers and Chemical Engineering. 56: 37-45. DOI: 10.1016/J.Compchemeng.2013.05.003  0.335
2012 Jia G, Stephanopoulos G, Gunawan R. Ensemble kinetic modeling of metabolic networks from dynamic metabolic profiles. Metabolites. 2: 891-912. PMID 24957767 DOI: 10.3390/Metabo2040891  0.796
2012 Jia G, Stephanopoulos G, Gunawan R. Incremental parameter estimation of kinetic metabolic network models. Bmc Systems Biology. 6: 142. PMID 23171810 DOI: 10.1186/1752-0509-6-142  0.785
2012 Poovathingal SK, Gruber J, Lakshmanan L, Halliwell B, Gunawan R. Is mitochondrial DNA turnover slower than commonly assumed? Biogerontology. 13: 557-64. PMID 22864459 DOI: 10.1007/S10522-012-9390-7  0.728
2012 Poovathingal SK, Gruber J, Ng LF, Halliwell B, Gunawan R. Maximizing signal-to-noise ratio in the random mutation capture assay. Nucleic Acids Research. 40: e35. PMID 22180539 DOI: 10.1093/Nar/Gkr1221  0.718
2012 Jia G, Gunawan R. Construction of kinetic model library of metabolic networks Ifac Proceedings Volumes (Ifac-Papersonline). 8: 952-957. DOI: 10.3182/20120710-4-Sg-2026.00189  0.384
2011 Jia G, Stephanopoulos GN, Gunawan R. Parameter estimation of kinetic models from metabolic profiles: two-phase dynamic decoupling method. Bioinformatics (Oxford, England). 27: 1964-70. PMID 21558155 DOI: 10.1093/Bioinformatics/Btr293  0.788
2011 Perumal TM, Gunawan R. Understanding dynamics using sensitivity analysis: caveat and solution. Bmc Systems Biology. 5: 41. PMID 21406095 DOI: 10.1186/1752-0509-5-41  0.315
2011 Perumal TM, Gunawan R. Impulse parametric sensitivity analysis Ifac Proceedings Volumes (Ifac-Papersonline). 18: 9686-9690. DOI: 10.3182/20110828-6-It-1002.03771  0.337
2010 Tam ZY, Cai YH, Gunawan R. Elucidating cytochrome C release from mitochondria: insights from an in silico three-dimensional model. Biophysical Journal. 99: 3155-63. PMID 21081062 DOI: 10.1016/J.Bpj.2010.09.041  0.771
2010 Poovathingal SK, Gunawan R. Global parameter estimation methods for stochastic biochemical systems. Bmc Bioinformatics. 11: 414. PMID 20691037 DOI: 10.1186/1471-2105-11-414  0.745
2010 Gruber J, Poovathingal SK, Schaffer S, Ng LF, Gunawan R, Halliwell B. Caenorhabditis elegans life span studies: the challenge of maintaining synchronous cohorts. Rejuvenation Research. 13: 347-9. PMID 20426619 DOI: 10.1089/Rej.2009.0943  0.703
2010 Srinath S, Gunawan R. Parameter identifiability of power-law biochemical system models. Journal of Biotechnology. 149: 132-40. PMID 20197073 DOI: 10.1016/J.Jbiotec.2010.02.019  0.749
2010 Hildebrandt S, Bagheri N, Gunawan R, Mirsky H, Shoemaker J, Taylor S, Petzold L, Doyle FJ. Systems Analysis for Systems Biology Systems Biomedicine. 249-272. DOI: 10.1016/B978-0-12-372550-9.00010-9  0.738
2009 Poovathingal SK, Gruber J, Halliwell B, Gunawan R. Stochastic drift in mitochondrial DNA point mutations: a novel perspective ex silico. Plos Computational Biology. 5: e1000572. PMID 19936024 DOI: 10.1371/Journal.Pcbi.1000572  0.728
2009 Perumal TM, Wu Y, Gunawan R. Dynamical analysis of cellular networks based on the Green's function matrix. Journal of Theoretical Biology. 261: 248-59. PMID 19660478 DOI: 10.1016/J.Jtbi.2009.07.037  0.353
2008 Taylor SR, Gunawan R, Petzold LR, Doyle FJ. Sensitivity Measures for Oscillating Systems: Application to Mammalian Circadian Gene Network. Ieee Transactions On Automatic Control. 53: 177-188. PMID 19593456 DOI: 10.1109/Tac.2007.911364  0.483
2008 Perumal TM, Wu Y, Gunawan R. Robustness analysis of cellular systems for in silico drug discovery Ifac Proceedings Volumes (Ifac-Papersonline). 17. DOI: 10.3182/20080706-5-Kr-1001.02133  0.335
2008 Gunawan R, Fusman I, Braatz RD. Parallel high-resolution finite volume simulation of particulate processes Aiche Journal. 54: 1449-1458. DOI: 10.1002/Aic.11484  0.488
2007 Gunawan R, Doyle FJ. Phase sensitivity analysis of circadian rhythm entrainment. Journal of Biological Rhythms. 22: 180-94. PMID 17440219 DOI: 10.1177/0748730407299194  0.463
2006 Gunawan R, Doyle FJ. Isochron-based phase response analysis of circadian rhythms. Biophysical Journal. 91: 2131-41. PMID 16815910 DOI: 10.1529/Biophysj.105.078006  0.436
2006 Braatz RD, Alkire RC, Seebauer E, Rusli E, Gunawan R, Drews TO, Li X, He Y. Perspectives on the design and control of multiscale systems Journal of Process Control. 16: 193-204. DOI: 10.1016/S1474-6670(17)31806-2  0.774
2006 Doyle FJ, Gunawan R, Bagheri N, Mirsky H, To TL. Circadian rhythm: A natural, robust, multi-scale control system Computers and Chemical Engineering. 30: 1700-1711. DOI: 10.1016/J.Compchemeng.2006.05.029  0.612
2006 Braatz RD, Alkire RC, Seebauer EG, Drews TO, Rusli E, Karulkar M, Xue F, Qin Y, Jung MYL, Gunawan R. A multiscale systems approach to microelectronic processes Computers and Chemical Engineering. 30: 1643-1656. DOI: 10.1016/J.Compchemeng.2006.05.022  0.762
2005 Gadkar KG, Gunawan R, Doyle FJ. Iterative approach to model identification of biological networks. Bmc Bioinformatics. 6: 155. PMID 15967022 DOI: 10.1186/1471-2105-6-155  0.503
2005 Gunawan R, Cao Y, Petzold L, Doyle FJ. Sensitivity analysis of discrete stochastic systems. Biophysical Journal. 88: 2530-40. PMID 15695639 DOI: 10.1529/Biophysj.104.053405  0.5
2005 Gunawan R, Doyle FJ. Phase sensitivity analysis of a circadian rhythm gene network Proceedings of the 44th Ieee Conference On Decision and Control, and the European Control Conference, Cdc-Ecc '05. 2005: 3687-3692. DOI: 10.1109/CDC.2005.1582735  0.418
2005 Gunawan R, Doyle FJ. Isochron-based phase sensitivity analysis of oscillatory biological systems Aiche Annual Meeting, Conference Proceedings. 11701-11713.  0.36
2004 Jung MYL, Gunawan R, Braatz RD, Seebauer EG. A simplified picture for transient enhanced diffusion of boron in silicon Journal of the Electrochemical Society. 151. DOI: 10.1149/1.1628238  0.644
2004 Jung MYL, Gunawan R, Braatz RD, Seebauer EG. Effect of near-surface band bending on dopant profiles in ion-implanted silicon Journal of Applied Physics. 95: 1134-1140. DOI: 10.1063/1.1638621  0.601
2004 Gunawan R, Jung M, Seebauer E, Braatz R. Optimal Control of Transient Enhanced Diffusion Ifac Proceedings Volumes. 37: 547-552. DOI: 10.1016/S1474-6670(17)38789-X  0.622
2004 Gadkar KG, Gunawan R, Doyle FJ. Modeling and Analysis Challenges in Systems Biology Ifac Proceedings Volumes. 37: 1-11. DOI: 10.1016/S1474-6670(17)32551-X  0.544
2004 Braatz R, Alkire R, Seebauer E, Rusli E, Gunawan R, Drews T, Li X, He Y. Perspectives on the Design and Control of Multiscale Systems Ifac Proceedings Volumes. 37: 155-166. DOI: 10.1016/S1474-6670(17)31806-2  0.76
2004 Gunawan R, Jung MYL, Seebauer EG, Braatz RD. Optimal control of rapid thermal annealing in a semiconductor process Journal of Process Control. 14: 423-430. DOI: 10.1016/J.Jprocont.2003.07.005  0.628
2004 Gunawan R, Fusman I, Braatz RD. High resolution algorithms for multidimensional population balance equations Aiche Journal. 50: 2738-2749. DOI: 10.1002/Aic.10228  0.468
2004 Jung MYL, Gunawan R, Braatz RD, Seebauer EG. Pair diffusion and kick-out: Contributions to diffusion of boron in silicon Aiche Journal. 50: 3248-3256. DOI: 10.1002/Aic.10220  0.628
2004 Braatz RD, Fujiwara M, Hukkanen EJ, Pirkle JC, Togkalidou T, Gunawan R. A holistic approach to chemical process design and development Asee Annual Conference Proceedings. 6525-6537.  0.748
2003 Jung MYL, Gunawan R, Braatz RD, Seebauer EG. Ramp-rate effects on transient enhanced diffusion and dopant activation Journal of the Electrochemical Society. 150. DOI: 10.1149/1.1627354  0.614
2003 Gunawan R, Jung MYL, Braatz RD, Seebauer EG. Parameter sensitivity analysis applied to modeling transient enhanced diffusion and activation of boron in silicon Journal of the Electrochemical Society. 150. DOI: 10.1149/1.1619992  0.654
2003 Dev K, Jung MYL, Gunawan R, Braatz RD, Seebauer EG. Mechanism for coupling between properties of interfaces and bulk semiconductors Physical Review B. 68. DOI: 10.1103/Physrevb.68.195311  0.61
2003 Gunawan R, Jung MYL, Seebauer EG, Braatz RD. Maximum a posteriori estimation of transient enhanced diffusion energetics Aiche Journal. 49: 2114-2123. DOI: 10.1002/Aic.690490819  0.65
2003 Dev K, Jung MYL, Gunawan R, Braatz RD, Seebauer EG. Mechanism for coupling between properties of interfaces and bulk semiconductors Physical Review B - Condensed Matter and Materials Physics. 68: 1953111-1953116.  0.432
2002 GUNAWAN R, MA DL, FUJIWARA M, BRAATZ RD. IDENTIFICATION OF KINETIC PARAMETERS IN MULTIDIMENSIONAL CRYSTALLIZATION PROCESSES International Journal of Modern Physics B. 16: 367-374. DOI: 10.1142/S0217979202009883  0.486
2002 Gunawan R, Jung MYL, Braatz RD, Seebauer EG. Systems analysis applied to modeling dopant activation and TED in rapid thermal annealing 10th Ieee International Conference On Advanced Thermal Processing of Semiconductors, Rtp 2002. 107-110. DOI: 10.1109/RTP.2002.1039447  0.645
2002 Gunawan R, Ma DL, Fujiwara M, Braatz RD. Identification of kinetic parameters in multidimensional crystallization processes International Journal of Modern Physics B. 16: 367-374.  0.382
2001 Gunawan R, Russell EL, Braatz RD. Comparison of theoretical and computational characteristics of dimensionality reduction methods for large-scale uncertain systems Journal of Process Control. 11: 543-552. DOI: 10.1016/S0959-1524(00)00024-X  0.48
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