Rudiyanto Gunawan

发表

Global parameter estimation methods for stochastic biochemical systems

Suresh Kumar Poovathingal, Rudiyanto Gunawan, S. Poovathingal, 2010, BMC Bioinformatics.

Special Issue on “Biological Networks”

Rudiyanto Gunawan, Neda Bagheri, 2018 .

Parameter estimation of dynamic biological network models using integrated fluxes

Yang Liu, Rudiyanto Gunawan, Rudiyanto Gunawan, 2014, BMC Systems Biology.

Context-Dependent Role of Mitochondrial Fusion-Fission in Clonal Expansion of mtDNA Mutations

Rudiyanto Gunawan, Barry Halliwell, Zhi Yang Tam, 2015, PLoS Comput. Biol..

Gene Regulatory Network Inference Using Time-Stamped Cross-Sectional Single Cell Expression Data

Rudiyanto Gunawan, Nan Papili Gao, S. M. Minhaz Ud-Dean, 2016 .

Iterative approach to model identification of biological networks

Rudiyanto Gunawan, Francis J. Doyle, Kapil G. Gadkar, 2005, BMC Bioinformatics.

SINCERITIES: inferring gene regulatory networks from time-stamped single cell transcriptional expression profiles

Rudiyanto Gunawan, Olivier Gandrillon, Nan Papili Gao, 2016, bioRxiv.

Optimal control of rapid thermal annealing in a semiconductor process

Richard D. Braatz, Rudiyanto Gunawan, Edmund G Seebauer, 2004 .

Stochastic Drift in Mitochondrial DNA Point Mutations: A Novel Perspective Ex Silico

Suresh Kumar Poovathingal, Rudiyanto Gunawan, Barry Halliwell, 2009, PLoS Comput. Biol..

Optimal design of gene knockout experiments for gene regulatory network inference

Rudiyanto Gunawan, S. M. Minhaz Ud-Dean, Rudiyanto Gunawan, 2015, Bioinform..

Perspectives on the design and control of multiscale systems

Richard D. Braatz, Rudiyanto Gunawan, Effendi Rusli, 2004 .

Systems Analysis for Systems Biology

Rudiyanto Gunawan, Francis J. Doyle, Linda R. Petzold, 2010 .

Ensemble Kinetic Modeling of Metabolic Networks from Dynamic Metabolic Profiles

Rudiyanto Gunawan, Gregory Stephanopoulos, Gengjie Jia, 2012, Metabolites.

Parameter identifiability of power-law biochemical system models.

Rudiyanto Gunawan, Sridharan Srinath, Rudiyanto Gunawan, 2010, Journal of biotechnology.

Inferring gene targets of drugs and chemical compounds from gene expression profiles

Rudiyanto Gunawan, Heeju Noh, Rudiyanto Gunawan, 2016, Bioinform..

Introduction to Editorial Board Member: Professor Francis J. Doyle III

Rudiyanto Gunawan, Neda Bagheri, 2017, Bioengineering & Translational Medicine.

Perspectives on the design and control of multiscale systems

Richard D. Braatz, Rudiyanto Gunawan, Effendi Rusli, 2004 .

Parameter estimation of kinetic models from metabolic profiles: two-phase dynamic decoupling method

Rudiyanto Gunawan, Gregory Stephanopoulos, Gengjie Jia, 2011, Bioinform..

Un acercamiento holístico al diseño de procesos de materiales

David L. Ma, Richard D. Braatz, Rudiyanto Gunawan, 2002 .

Incremental parameter estimation of kinetic metabolic network models

Rudiyanto Gunawan, Gregory Stephanopoulos, Gengjie Jia, 2012, BMC Systems Biology.

Understanding dynamics using sensitivity analysis: caveat and solution

Rudiyanto Gunawan, Thanneer Malai Perumal, Rudiyanto Gunawan, 2011, BMC Systems Biology.

A multiscale systems approach to microelectronic processes

Richard D. Braatz, Rudiyanto Gunawan, Feng Xue, 2006, Comput. Chem. Eng..

Automatic Control in Systems Biology

Rudiyanto Gunawan, Francis J. Doyle, Jörg Stelling, 2009, Handbook of Automation.

Methods to Identify Cellular Architecture and Dynamics from Experimental Data

Rudiyanto Gunawan, Francis J. Doyle, Kapil G. Gadkar, 2006 .

Bioprocess optimization under uncertainty using ensemble modeling.

Rudiyanto Gunawan, Yang Liu, Rudiyanto Gunawan, 2017, Journal of biotechnology.

TRaCE+: Ensemble inference of gene regulatory networks from transcriptional expression profiles of gene knock-out experiments

Sandra Heise, Steffen Klamt, Rudiyanto Gunawan, 2016, BMC Bioinformatics.

Reduction of kinetic models using dynamic sensitivities

Rudiyanto Gunawan, Thanneer Malai Perumal, Sashikant Madgula Krishna, 2013, Comput. Chem. Eng..

Sensitivity Measures for Oscillating Systems: Application to Mammalian Circadian Gene Network

Rudiyanto Gunawan, Francis J. Doyle, Linda R. Petzold, 2008, IEEE Transactions on Automatic Control.

Circadian rhythm: A natural, robust, multi-scale control system

Rudiyanto Gunawan, Francis J. Doyle, Neda Bagheri, 2006, Comput. Chem. Eng..

REDEMPTION: reduced dimension ensemble modeling and parameter estimation

Yang Liu, Rudiyanto Gunawan, Erica Manesso, 2015, Bioinform..

DeltaNeTS+: elucidating the mechanism of drugs and diseases using gene expression and transcriptional regulatory networks

Rudiyanto Gunawan, Heeju Noh, Jason E. Shoemaker, 2021, BMC Bioinform..

Network perturbation analysis of gene transcriptional profiles reveals protein targets and mechanism of action of drugs and influenza A viral infection

Rudiyanto Gunawan, Heeju Noh, Jason E Shoemaker, 2017, bioRxiv.

Mechanism for coupling between properties of interfaces and bulk semiconductors

Richard D. Braatz, Rudiyanto Gunawan, Kapil Dev, 2003 .

Ensemble Inference and Inferability of Gene Regulatory Networks

Rudiyanto Gunawan, S. M. Minhaz Ud-Dean, Rudiyanto Gunawan, 2014, PloS one.

Phase Sensitivity Analysis of Circadian Rhythm Entrainment

Rudiyanto Gunawan, Francis J Doyle, F. Doyle, 2007, Journal of biological rhythms.

Assessment of Network Inference Methods: How to Cope with an Underdetermined Problem

Rudiyanto Gunawan, Rudiyanto Gunawan, Caroline Siegenthaler, 2014, PloS one.

Elucidating Cellular Population Dynamics by Molecular Density Function Perturbations

Rudiyanto Gunawan, Thanneer M. Perumal, Rudiyanto Gunawan, 2018 .

Network perturbation analysis of gene transcriptional profiles reveals protein targets and mechanism of action of drugs and influenza A viral infection

Rudiyanto Gunawan, Heeju Noh, Jason E. Shoemaker, 2017 .

Isochron-based phase response analysis of circadian rhythms.

Rudiyanto Gunawan, Francis J Doyle, F. Doyle, 2006, Biophysical journal.

A Simplified Picture for Transient Enhanced Diffusion of Boron in Silicon

Richard D. Braatz, Rudiyanto Gunawan, Edmund G Seebauer, 2004 .

Systems analysis applied to modeling dopant activation and TED in rapid thermal annealing

Richard D. Braatz, Rudiyanto Gunawan, Edmund G Seebauer, 2002, 10th IEEE International Conference of Advanced Thermal Processing of Semiconductors.

Multi-Objective Optimization of Experiments Using Curvature and Fisher Information Matrix

Rudiyanto Gunawan, Rudiyanto Gunawan, Srinath Sridharan, 2017 .

Spherical Crystallization of Glycine from Monodisperse Microfluidic Emulsions

Rudiyanto Gunawan, T. Alan Hatton, Raj Rajagopalan, 2012 .

CALISTA: Clustering and LINEAGE Inference in Single-Cell Transcriptional Analysis

Rudiyanto Gunawan, Thomas Hartmann, N. Gao, 2018, bioRxiv.

Dynamical analysis of cellular networks based on the Green's function matrix.

Rudiyanto Gunawan, Thanneer M Perumal, Rudiyanto Gunawan, 2009, Journal of theoretical biology.

Comparison of theoretical and computational characteristics of dimensionality reduction methods for large-scale uncertain systems

Richard D. Braatz, Rudiyanto Gunawan, Evan L. Russell, 2001 .

Parallel high‐resolution finite volume simulation of particulate processes

Richard D. Braatz, Rudiyanto Gunawan, R. Braatz, 2008 .