Publication

A Design-Build-Test cycle using modeling and experiments reveals interdependencies between upper glycolysis and xylose uptake in recombinant S. cerevisiae and improves predictive capabilities of large-scale kinetic models

Publications associées (30)

Code Generation Approach Supporting Complex System Modeling based on Graph Pattern Matching

Code generation is an effective way to drive the complex system development in model-based systems engineering. Currently, different code generators are developed for different modeling languages to deal with the development of systems with multi-domain. T ...

ELSEVIER2022

Model-based Systems Engineering Papers Analysis based on Word Cloud Visualization

Dimitrios Kyritsis, Jinzhi Lu, Xiaochen Zheng

With the continuous improvement of system scale and complexity, model-based system engineering (MBSE) is of great importance in the practice of system engineering (SE). MBSE has been widely concerned in industry, especially in the field of complex equipmen ...

IEEE2022

Computational tools and resources for designing new pathways to small molecules

Vassily Hatzimanikatis, Anastasia Sveshnikova

The metabolic engineering community relies on computational methods for pathway design to produce important small molecules in microbial hosts. Metabolic network databases are continuously curated and updated with known and novel reactions that expand the ...

CURRENT BIOLOGY LTD2022

Model-based scale-up of a continuously operated consolidated bioprocess based on a microbial consortium for the production of ethanol

David Beat Dempfle

This work demonstrated that consolidated bioprocessing is a promising concept for conversion of lignocellulose to ethanol at industrial scale. CBP offers great cost saving potential, is feasible to be operated continuously and may be scaled up due to exten ...

EPFL2022

Class I histone deacetylases (HDAC1-3) are histone lysine delactylases

Di Zhang, Alexander Lund Nielsen, Carlos Moreno Yruela

Lysine L-lactylation [K(L-la)] is a newly discovered histone mark stimulated under conditions of high glycolysis, such as the Warburg effect. K(L-la) is associated with functions that are different from the widely studied histone acetylation. While K(L-la) ...

2022

The effects of model complexity and size on metabolic flux distribution and control: case study in Escherichia coli

Vassily Hatzimanikatis, Georgios Fengos, Tuure Eelis Hameri

Background Significant efforts have been made in building large-scale kinetic models of cellular metabolism in the past two decades. However, most kinetic models published to date, remain focused around central carbon pathways or are built around ad hoc re ...

BMC2021

Hyperpolarized C-13-glucose magnetic resonance highlights reduced aerobic glycolysis in vivo in infiltrative glioblastoma

Arnaud Comment, Bernard Lanz, Rolf Gruetter, Cristina Ramona Cudalbu, Mor-Miri Mishkovsky, Jocelyne Bloch

Glioblastoma (GBM) is the most aggressive brain tumor type in adults. GBM is heterogeneous, with a compact core lesion surrounded by an invasive tumor front. This front is highly relevant for tumor recurrence but is generally non-detectable using standard ...

Nature Research2021

Constraint-based metabolic control analysis for rational strain engineering

Ljubisa Miskovic, Vassily Hatzimanikatis, Meriç Ataman, Tuure Eelis Hameri, Sofia Tsouka

The advancements in genome editing techniques over the past years have rekindled interest in rational metabolic engineering strategies. While Metabolic Control Analysis (MCA) is a well-established method for quantifying the effects of metabolic engineering ...

2021

Sustainable green processing of grape pomace for the production of value-added products: An overview

Edgard Gnansounou

In recent years, the recovery of valuable compounds from food waste like grape pomace is an emerging issue in the food sector. Grape pomace or marc can be considered as an important solid waste that is produced from the wine industries after the pressing a ...

ELSEVIER2021

Design Ontology Supporting Model-Based Systems Engineering Formalisms

Dimitrios Kyritsis, Jinzhi Lu, Xiaochen Zheng, Han Li

Model-based systems engineering (MBSE) provides an important capability for managing the complexities of system development. MBSE empowers the formalism of system architectures for supporting model-based requirement elicitation, specification, design, deve ...

IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC2022