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List of works by Rudiyanto Gunawan

Are mutagenic non D-loop direct repeat motifs in mitochondrial DNA under a negative selection pressure?

scientific article published on 8 April 2015

Assessing and Resolving Model Misspecifications in Metabolic Flux Analysis

scientific article published on 24 May 2017

Assessment of network inference methods: how to cope with an underdetermined problem

scientific article

Caenorhabditis elegans life span studies: the challenge of maintaining synchronous cohorts

scientific article published on April 2010

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

scientific article published on 21 May 2015

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

scientific article published on 04 March 2021

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

scientific article

Elucidating cytochrome C release from mitochondria: insights from an in silico three-dimensional model

scientific article

Ensemble inference and inferability of gene regulatory networks

scientific article

Ensemble kinetic modeling of metabolic networks from dynamic metabolic profiles

scientific article published on 12 November 2012

Global parameter estimation methods for stochastic biochemical systems ⬇️

scientific article published on August 6, 2010

Glycosylation flux analysis reveals dynamic changes of intracellular glycosylation flux distribution in Chinese hamster ovary fed-batch cultures.

scientific article published on 25 July 2017

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

scientific article

Is mitochondrial DNA turnover slower than commonly assumed?

scientific article published on 3 August 2012

Isochron-based phase response analysis of circadian rhythms

scientific article published on 30 June 2006

Kinetic Modeling of Mammalian Cell Culture Bioprocessing: The Quest to Advance Biomanufacturing

scientific article published on 13 October 2017

Mathematical modeling of the role of mitochondrial fusion and fission in mitochondrial DNA maintenance

scientific article

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

scientific article published on 9 January 2018

Optimal design of gene knockout experiments for gene regulatory network inference.

scientific article published on 14 November 2015

Parameter estimation of dynamic biological network models using integrated fluxes.

scientific article

Parameter identifiability of power-law biochemical system models

scientific article

Role of direct repeat and stem-loop motifs in mtDNA deletions: cause or coincidence?

scientific article

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

scientific article published on 14 September 2017

Single-Cell-Based Analysis Highlights a Surge in Cell-to-Cell Molecular Variability Preceding Irreversible Commitment in a Differentiation Process

scientific article

Stochastic drift in mitochondrial DNA point mutations: a novel perspective ex silico

scientific article

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

scientific article

Understanding dynamics using sensitivity analysis: caveat and solution ⬇️

scientific article published on March 15, 2011

Using dynamic sensitivities to characterize metabolic reaction systems

scientific article published on 15 September 2015

ΔFBA-Predicting metabolic flux alterations using genome-scale metabolic models and differential transcriptomic data

scientific article published on 10 November 2021

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