BibTeX records: Rudiyanto Gunawan

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@article{DBLP:journals/bioinformatics/GrothDGN22,
  author       = {Theodore Groth and
                  Alexander D. Diehl and
                  Rudiyanto Gunawan and
                  Sriram Neelamegham},
  title        = {GlycoEnzOnto: a GlycoEnzyme pathway and molecular function ontology},
  journal      = {Bioinform.},
  volume       = {38},
  number       = {24},
  pages        = {5413--5420},
  year         = {2022},
  url          = {https://doi.org/10.1093/bioinformatics/btac704},
  doi          = {10.1093/BIOINFORMATICS/BTAC704},
  timestamp    = {Sat, 13 May 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/GrothDGN22.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bmcbi/NohHCSG21,
  author       = {Heeju Noh and
                  Ziyi Hua and
                  Panagiotis Chrysinas and
                  Jason E. Shoemaker and
                  Rudiyanto Gunawan},
  title        = {DeltaNeTS+: elucidating the mechanism of drugs and diseases using
                  gene expression and transcriptional regulatory networks},
  journal      = {{BMC} Bioinform.},
  volume       = {22},
  number       = {1},
  pages        = {108},
  year         = {2021},
  url          = {https://doi.org/10.1186/s12859-021-04046-2},
  doi          = {10.1186/S12859-021-04046-2},
  timestamp    = {Sun, 12 Nov 2023 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bmcbi/NohHCSG21.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/ploscb/RaviG21,
  author       = {Sudharshan Ravi and
                  Rudiyanto Gunawan},
  title        = {{\(\Delta\)}FBA - Predicting metabolic flux alterations using genome-scale
                  metabolic models and differential transcriptomic data},
  journal      = {PLoS Comput. Biol.},
  volume       = {17},
  number       = {11},
  year         = {2021},
  url          = {https://doi.org/10.1371/journal.pcbi.1009589},
  doi          = {10.1371/JOURNAL.PCBI.1009589},
  timestamp    = {Tue, 16 Aug 2022 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/ploscb/RaviG21.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bioinformatics/GaoUGG18,
  author       = {Nan Papili Gao and
                  S. M. Minhaz Ud{-}Dean and
                  Olivier Gandrillon and
                  Rudiyanto Gunawan},
  title        = {{SINCERITIES:} inferring gene regulatory networks from time-stamped
                  single cell transcriptional expression profiles},
  journal      = {Bioinform.},
  volume       = {34},
  number       = {2},
  pages        = {258--266},
  year         = {2018},
  url          = {https://doi.org/10.1093/bioinformatics/btx575},
  doi          = {10.1093/BIOINFORMATICS/BTX575},
  timestamp    = {Mon, 02 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/GaoUGG18.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bioinformatics/Ud-DeanG16,
  author       = {S. M. Minhaz Ud{-}Dean and
                  Rudiyanto Gunawan},
  title        = {Optimal design of gene knockout experiments for gene regulatory network
                  inference},
  journal      = {Bioinform.},
  volume       = {32},
  number       = {6},
  pages        = {875--883},
  year         = {2016},
  url          = {https://doi.org/10.1093/bioinformatics/btv672},
  doi          = {10.1093/BIOINFORMATICS/BTV672},
  timestamp    = {Mon, 02 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/Ud-DeanG16.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bioinformatics/NohG16,
  author       = {Heeju Noh and
                  Rudiyanto Gunawan},
  title        = {Inferring gene targets of drugs and chemical compounds from gene expression
                  profiles},
  journal      = {Bioinform.},
  volume       = {32},
  number       = {14},
  pages        = {2120--2127},
  year         = {2016},
  url          = {https://doi.org/10.1093/bioinformatics/btw148},
  doi          = {10.1093/BIOINFORMATICS/BTW148},
  timestamp    = {Mon, 02 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/NohG16.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bmcbi/Ud-DeanHKG16,
  author       = {S. M. Minhaz Ud{-}Dean and
                  Sandra Heise and
                  Steffen Klamt and
                  Rudiyanto Gunawan},
  title        = {TRaCE+: Ensemble inference of gene regulatory networks from transcriptional
                  expression profiles of gene knock-out experiments},
  journal      = {{BMC} Bioinform.},
  volume       = {17},
  pages        = {252},
  year         = {2016},
  url          = {https://doi.org/10.1186/s12859-016-1137-z},
  doi          = {10.1186/S12859-016-1137-Z},
  timestamp    = {Sun, 15 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bmcbi/Ud-DeanHKG16.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bioinformatics/LiuMG15,
  author       = {Yang Liu and
                  Erica Manesso and
                  Rudiyanto Gunawan},
  title        = {{REDEMPTION:} reduced dimension ensemble modeling and parameter estimation},
  journal      = {Bioinform.},
  volume       = {31},
  number       = {20},
  pages        = {3387--3389},
  year         = {2015},
  url          = {https://doi.org/10.1093/bioinformatics/btv365},
  doi          = {10.1093/BIOINFORMATICS/BTV365},
  timestamp    = {Mon, 02 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/LiuMG15.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/ploscb/TamGHG15,
  author       = {Zhi Yang Tam and
                  Jan Gruber and
                  Barry Halliwell and
                  Rudiyanto Gunawan},
  title        = {Context-Dependent Role of Mitochondrial Fusion-Fission in Clonal Expansion
                  of mtDNA Mutations},
  journal      = {PLoS Comput. Biol.},
  volume       = {11},
  number       = {5},
  year         = {2015},
  url          = {https://doi.org/10.1371/journal.pcbi.1004183},
  doi          = {10.1371/JOURNAL.PCBI.1004183},
  timestamp    = {Mon, 26 Oct 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/ploscb/TamGHG15.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bmcsb/LiuG14,
  author       = {Yang Liu and
                  Rudiyanto Gunawan},
  title        = {Parameter estimation of dynamic biological network models using integrated
                  fluxes},
  journal      = {{BMC} Syst. Biol.},
  volume       = {8},
  pages        = {127},
  year         = {2014},
  url          = {https://doi.org/10.1186/s12918-014-0127-x},
  doi          = {10.1186/S12918-014-0127-X},
  timestamp    = {Tue, 05 May 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bmcsb/LiuG14.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/cce/PerumalKTG13,
  author       = {Thanneer Malai Perumal and
                  Sashikant Madgula Krishna and
                  Sai Sandeep Tallam and
                  Rudiyanto Gunawan},
  title        = {Reduction of kinetic models using dynamic sensitivities},
  journal      = {Comput. Chem. Eng.},
  volume       = {56},
  pages        = {37--45},
  year         = {2013},
  url          = {https://doi.org/10.1016/j.compchemeng.2013.05.003},
  doi          = {10.1016/J.COMPCHEMENG.2013.05.003},
  timestamp    = {Mon, 18 May 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/cce/PerumalKTG13.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bmcsb/JiaSG12,
  author       = {Gengjie Jia and
                  Gregory Stephanopoulos and
                  Rudiyanto Gunawan},
  title        = {Incremental parameter estimation of kinetic metabolic network models},
  journal      = {{BMC} Syst. Biol.},
  volume       = {6},
  pages        = {142},
  year         = {2012},
  url          = {https://doi.org/10.1186/1752-0509-6-142},
  doi          = {10.1186/1752-0509-6-142},
  timestamp    = {Tue, 05 May 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bmcsb/JiaSG12.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bioinformatics/JiaSG11,
  author       = {Gengjie Jia and
                  Gregory Stephanopoulos and
                  Rudiyanto Gunawan},
  title        = {Parameter estimation of kinetic models from metabolic profiles: two-phase
                  dynamic decoupling method},
  journal      = {Bioinform.},
  volume       = {27},
  number       = {14},
  pages        = {1964--1970},
  year         = {2011},
  url          = {https://doi.org/10.1093/bioinformatics/btr293},
  doi          = {10.1093/BIOINFORMATICS/BTR293},
  timestamp    = {Mon, 02 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/JiaSG11.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bmcsb/PerumalG11,
  author       = {Thanneer M. Perumal and
                  Rudiyanto Gunawan},
  title        = {Understanding dynamics using sensitivity analysis: caveat and solution},
  journal      = {{BMC} Syst. Biol.},
  volume       = {5},
  pages        = {41},
  year         = {2011},
  url          = {https://doi.org/10.1186/1752-0509-5-41},
  doi          = {10.1186/1752-0509-5-41},
  timestamp    = {Tue, 05 May 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bmcsb/PerumalG11.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bmcbi/PoovathingalG10,
  author       = {Suresh Kumar Poovathingal and
                  Rudiyanto Gunawan},
  title        = {Global parameter estimation methods for stochastic biochemical systems},
  journal      = {{BMC} Bioinform.},
  volume       = {11},
  pages        = {414},
  year         = {2010},
  url          = {https://doi.org/10.1186/1471-2105-11-414},
  doi          = {10.1186/1471-2105-11-414},
  timestamp    = {Mon, 26 Oct 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bmcbi/PoovathingalG10.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/ploscb/PoovathingalGHG09,
  author       = {Suresh Kumar Poovathingal and
                  Jan Gruber and
                  Barry Halliwell and
                  Rudiyanto Gunawan},
  title        = {Stochastic Drift in Mitochondrial {DNA} Point Mutations: {A} Novel
                  Perspective \emph{Ex Silico}},
  journal      = {PLoS Comput. Biol.},
  volume       = {5},
  number       = {11},
  year         = {2009},
  url          = {https://doi.org/10.1371/journal.pcbi.1000572},
  doi          = {10.1371/JOURNAL.PCBI.1000572},
  timestamp    = {Mon, 26 Oct 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/ploscb/PoovathingalGHG09.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@incollection{DBLP:reference/auto/MirskySGBTKSD09,
  author       = {Henry Mirsky and
                  J{\"{o}}rg Stelling and
                  Rudiyanto Gunawan and
                  Neda Bagheri and
                  Stephanie R. Taylor and
                  Eric Kwei and
                  Jason E. Shoemaker and
                  Francis J. Doyle III},
  editor       = {Shimon Y. Nof},
  title        = {Automatic Control in Systems Biology},
  booktitle    = {Springer Handbook of Automation},
  series       = {Springer Handbooks},
  pages        = {1335--1360},
  publisher    = {Springer},
  year         = {2009},
  url          = {https://doi.org/10.1007/978-3-540-78831-7\_75},
  doi          = {10.1007/978-3-540-78831-7\_75},
  timestamp    = {Tue, 12 Nov 2019 17:14:07 +0100},
  biburl       = {https://dblp.org/rec/reference/auto/MirskySGBTKSD09.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/tac/TaylorGPD08,
  author       = {Stephanie R. Taylor and
                  Rudiyanto Gunawan and
                  Linda R. Petzold and
                  Francis J. Doyle III},
  title        = {Sensitivity Measures for Oscillating Systems: Application to Mammalian
                  Circadian Gene Network},
  journal      = {{IEEE} Trans. Autom. Control.},
  volume       = {53},
  pages        = {177--188},
  year         = {2008},
  url          = {https://doi.org/10.1109/TAC.2007.911364},
  doi          = {10.1109/TAC.2007.911364},
  timestamp    = {Wed, 20 May 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/tac/TaylorGPD08.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/cce/BraatzASDRKXQJG06,
  author       = {Richard D. Braatz and
                  Richard C. Alkire and
                  Edmund G. Seebauer and
                  Timothy O. Drews and
                  Effendi Rusli and
                  Mohan Karulkar and
                  Feng Xue and
                  Yan Qin and
                  Michael Y. L. Jung and
                  Rudiyanto Gunawan},
  title        = {A multiscale systems approach to microelectronic processes},
  journal      = {Comput. Chem. Eng.},
  volume       = {30},
  number       = {10-12},
  pages        = {1643--1656},
  year         = {2006},
  url          = {https://doi.org/10.1016/j.compchemeng.2006.05.022},
  doi          = {10.1016/J.COMPCHEMENG.2006.05.022},
  timestamp    = {Mon, 18 May 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/cce/BraatzASDRKXQJG06.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/cce/DoyleGBMT06,
  author       = {Francis J. Doyle III and
                  Rudiyanto Gunawan and
                  Neda Bagheri and
                  Henry Mirsky and
                  Tsz Leung To},
  title        = {Circadian rhythm: {A} natural, robust, multi-scale control system},
  journal      = {Comput. Chem. Eng.},
  volume       = {30},
  number       = {10-12},
  pages        = {1700--1711},
  year         = {2006},
  url          = {https://doi.org/10.1016/j.compchemeng.2006.05.029},
  doi          = {10.1016/J.COMPCHEMENG.2006.05.029},
  timestamp    = {Mon, 18 May 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/cce/DoyleGBMT06.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bmcbi/GadkarGD05,
  author       = {Kapil G. Gadkar and
                  Rudiyanto Gunawan and
                  Francis J. Doyle III},
  title        = {Iterative approach to model identification of biological networks},
  journal      = {{BMC} Bioinform.},
  volume       = {6},
  pages        = {155},
  year         = {2005},
  url          = {https://doi.org/10.1186/1471-2105-6-155},
  doi          = {10.1186/1471-2105-6-155},
  timestamp    = {Sun, 15 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bmcbi/GadkarGD05.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/cdc/GunawanD05,
  author       = {Rudiyanto Gunawan and
                  Francis J. Doyle III},
  title        = {Phase Sensitivity Analysis of a Circadian Rhythm Gene Network},
  booktitle    = {44th {IEEE} {IEEE} Conference on Decision and Control and 8th European
                  Control Conference Control, {CDC/ECC} 2005, Seville, Spain, 12-15
                  December, 2005},
  pages        = {3687--3692},
  publisher    = {{IEEE}},
  year         = {2005},
  url          = {https://doi.org/10.1109/CDC.2005.1582735},
  doi          = {10.1109/CDC.2005.1582735},
  timestamp    = {Fri, 04 Mar 2022 13:25:54 +0100},
  biburl       = {https://dblp.org/rec/conf/cdc/GunawanD05.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/eucc/GunawanRB01,
  author       = {Rudiyanto Gunawan and
                  E. L. Russell and
                  Richard D. Braatz},
  title        = {Robustness analysis of multivariable systems with time delays},
  booktitle    = {6th European Control Conference, {ECC} 2001, Porto, Portugal, September
                  4-7, 2001},
  pages        = {1882--1887},
  publisher    = {{IEEE}},
  year         = {2001},
  url          = {https://doi.org/10.23919/ECC.2001.7076196},
  doi          = {10.23919/ECC.2001.7076196},
  timestamp    = {Mon, 15 Feb 2021 11:16:45 +0100},
  biburl       = {https://dblp.org/rec/conf/eucc/GunawanRB01.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

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