Publications by Ljubisa Miskovic

The Dawn of High-throughput and Genome-scale Kinetic Modeling: Recent Advances and Future Directions

Vassily Hatzimanikatis, Ljubisa Miskovic

Researchers have invested much effort into developing kinetic models due to their ability to capture dynamic behaviors, transient states, and regulatory mechanisms of metabolism, providing a detailed and realistic representation of cellular processes. Hist ...

AMER CHEMICAL SOC2025

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

Vassily Hatzimanikatis, Ljubisa Miskovic, Maria Masid Barcon, Francisco Javier Perez Saez, 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

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

Vassily Hatzimanikatis, Ljubisa Miskovic

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

Rational strain design with minimal phenotype perturbation

Vassily Hatzimanikatis, Ljubisa Miskovic, Daniel Robert Weilandt

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

Generative machine learning produces kinetic models that accurately characterize intracellular metabolic states

Vassily Hatzimanikatis, Ljubisa Miskovic

Generating large omics datasets has become routine for gaining insights into cellular processes, yet deciphering these datasets to determine metabolic states remains challenging. Kinetic models can help integrate omics data by explicitly linking metabolite ...

Springer Science and Business Media LLC2024

Supplementary datasets for the manuscript "Generative machine learning produces kinetic models that accurately characterize intracellular metabolic states" -Part 2

Vassily Hatzimanikatis, Ljubisa Miskovic, 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. The code to use with these da ...

Zenodo2023

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

Vassily Hatzimanikatis, Ljubisa Miskovic, 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

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

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

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

Reconstructing Kinetic Models for Dynamical Studies of Metabolism using Generative Adversarial Networks

Vassily Hatzimanikatis, Ljubisa Miskovic, Daniel Robert Weilandt, Pierre Guy Rémy Salvy

Kinetic models of metabolism relate metabolic fluxes, metabolite concentrations and enzyme levels through mechanistic relations, rendering them essential for understanding, predicting and optimizing the behaviour of living organisms. However, due to the la ...

NATURE PORTFOLIO2022

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

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

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