Publications de Mohammadomid Oftadeh

Designing pathways for bioproducing complex chemicals by combining tools for pathway extraction and ranking

Vassily Hatzimanikatis, Anastasia Sveshnikova, Mohammadomid Oftadeh

The synthesis of many important biochemicals involves complex molecules and numerous reactions. The design and optimization of whole-cell biocatalysts for the production of these molecules requires metabolic modeling to extract production pathways from bio ...

Springer Science and Business Media LLC2025

Genome-scale models of metabolism and expression predict the metabolic burden of recombinant protein expression

Vassily Hatzimanikatis, Mohammadomid Oftadeh

The production of recombinant proteins in a host using synthetic constructs such as plasmids comes at the cost of detrimental effects such as reduced growth, energetic inefficiencies, and other stress responses, collectively known as metabolic burden. Incr ...

2024

Modeling, analysis, and design of complex biological networks

Mohammadomid Oftadeh

Automating experimental procedures has resulted in an unprecedented increase in the volume of generated data, which, in turn, has caused an accumulation of unprocessed data. As a result, the need to develop tools to analyze data systematically has been ris ...

EPFL2023

From microbiome composition to functional engineering, one step at a time

Vassily Hatzimanikatis, Asli Sahin, Mohammadomid Oftadeh, Evangelia Vagena

Communities of microorganisms (microbiota) are present in all habitats on Earth and are relevant for agriculture, health, and climate. Deciphering the mechanisms that determine microbiota dynamics and functioning within the context of their respective envi ...

Amer Soc Microbiology2023

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