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Ljubisa Miskovic

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Publications associées (35)

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Dataset - Generative Approaches to Kinetic Parameter Inference in Metabolic Networks via Latent Space Exploration

Oussama Gabouj, Vassily Hatzimanikatis, Ljubisa Miskovic, Subham Choudhury, Ilias Toumpe

Dataset needed to reproduce the results in the manuscript by "Generative Approaches to Kinetic Parameter Inference in Metabolic Networks via Latent Space Exploration" by S. Choudhury et al. (under review, a preprint available at https://www.biorxiv.org/con ...

Zenodo2025

Identification of a Two-Input System: Variance Analysis

Dominique Bonvin, Alireza Karimi, Ljubisa Miskovic

This paper examines the identification of a single-output two-input system. Motivated by an experiment design problem(should one excite the two inputs simultaneously or separately), we examine the effect of the (second) input signal on the variance of the ...

2005

Dataset - Kinetic-model-guided engineering of multiple S. cerevisiae strains improves p-coumaric acid production

Vassily Hatzimanikatis, Ljubisa Miskovic, Francisco Javier Perez Saez, Maria Masid Barcon, Bharath Narayanan, Wei Jiang

Dataset supporting the results presented in the paper entitled "Kinetic-model-guided engineering of multiple S. cerevisiae strains improves p-coumaric acid production" by Narayanan, Jiang & Wang et al (https://doi.org/10.1016/j.ymben.2025.06.008). Dataset ...

Zenodo2025

A genome-scale metabolic model of Saccharomyces cerevisiae that integrates expression constraints and reaction thermodynamics

Vassily Hatzimanikatis, Ljubisa Miskovic, Maria Masid Barcon, Pierre Guy Rémy Salvy, Mohammadomid Oftadeh

Eukaryotic organisms play an important role in industrial biotechnology, from the production of fuels and commodity chemicals to therapeutic proteins. To optimize these industrial systems, a mathematical approach can be used to integrate the description of ...

Nature Portfolio2021

Direct Closed-Loop Identification of Multi-Input Systems: Variance Analysis

Dominique Bonvin, Alireza Karimi, Ljubisa Miskovic

An analysis of the variance of the parameters of a multi-input plant estimated in closed-loop operation is performed. More specifically, the effect of the simultaneous excitation of an additional input on the variance of the estimated parameters is investi ...

2006

Rational strain design with minimal phenotype perturbation

Vassily Hatzimanikatis, Ljubisa Miskovic, Daniel Robert Weilandt, Bharath Narayanan

Devising genetic interventions for desired cellular phenotypes remains challenging regarding time and resources. Kinetic models can accelerate this task by simulating metabolic responses to genetic perturbations. However, exhaustive design evaluations with ...

Nature Portfolio2024

Supplementary dataset for Enzyme promiscuous profiles for protein sequence and reaction annotation

Vassily Hatzimanikatis, Ljubisa Miskovic, Anastasia Sveshnikova, Homa Mohammadi Peyhani

The data and scripts used to produce, analyze, and visualize the results of the manuscript Enzyme promiscuous profiles for protein sequence and reaction annotation by Homa MohammadiPeyhani, Anastasia Sveshnikova, Ljubisa Miskovic, and Vassily Hatzimanikati ...

Zenodo2023

Correlation-Based Tuning of Decoupling Multivariable Controllers

Dominique Bonvin, Alireza Karimi, Ljubisa Miskovic

The iterative data-driven method labelled Correlation-based Tuning (CbT) is considered in this paper for the tuning of linear time-invariant multivariable controllers. The approach allows one to tune some elements of the controller transfer function matrix ...

2007

Perturbation rejection control strategy for OWL

Ljubisa Miskovic

The control system of the ESO 100 m telescope (OWL) has to reject slow and fast perturbations in several subsystems. In this paper we focus on the wind rejection control strategies for two subsystems: the main axes and the segmented mirror. It is shown tha ...

2006

On the Input Design for Data-Driven Correlation-Based Tuning of Multivariable Controllers

Dominique Bonvin, Alireza Karimi, Ljubisa Miskovic

An iterative data-driven correlation-based method has been proposed recently to tune multivariable linear time-invariant controllers in closed-loop operation. In this contribution, the preferred way of exciting a 2 × 2 system is investigated via the accura ...

2006

Supplementary datasets for the manuscript "Generative machine learning produces kinetic models that accurately characterize intracellular metabolic states" - Part 3

Vassily Hatzimanikatis, Ljubisa Miskovic, Subham Choudhury, Michaël Roger Germain Moret

Supplementary files containing datasets needed to reproduce the results of the manuscript "Generative machine learning produces kinetic models that accurately characterize intracellular metabolic states" by S. Choudhury et al (https://doi.org/10.1101/2023. ...

Zenodo2023

Rites of passage: requirements and standards for building kinetic models of metabolic phenotypes

Vassily Hatzimanikatis, Ljubisa Miskovic, Georgios Fengos, Milenko Tokic

The overarching ambition of kinetic metabolic modeling is to capture the dynamic behavior of metabolism to such an extent that systems and synthetic biology strategies can reliably be tested in silico. The lack of kinetic data hampers the development of ki ...

Elsevier2015

Closed-loop Identification of Multivariable Systems: With or Without Excitation of All References?

Dominique Bonvin, Alireza Karimi, Ljubisa Miskovic

A variance analysis of the parameters of a plant, belonging to a class of multivariable systems, estimated in closed-loop operation is performed. More specifically, having in mind the control applications where it is not desirable to excite all external re ...

2008

Identification of multi-input systems: variance analysis and input design issues

Dominique Bonvin, Alireza Karimi, Ljubisa Miskovic

This paper examines the identification of multi-input systems. Motivated by an experiment design problem (should one excite the various inputs simultaneously or separately), we examine the effect of an additional input on the variance of the estimated coef ...

2006

Correlation-Based Tuning of Linear Multivariable Decoupling Controllers

Dominique Bonvin, Alireza Karimi, Ljubisa Miskovic

The recently-proposed method for iterative correlation-based controller tuning is considered in this paper for the tuning of multivariable Linear Time-Invariant (LTI) controllers. The parameters of the controller are updated directly using the data acquire ...

2005