Publications de Noushin Hadadi

A workflow for annotating the knowledge gaps in metabolic reconstructions using known and hypothetical reactions

Vassily Hatzimanikatis, Meriç Ataman, Jasmin Maria Hafner, Homa Mohammadi Peyhani, Evangelia Vagena, Noushin Hadadi, Anush Chiappino-Pepe

Advances in medicine and biotechnology rely on a deep understanding of biological processes. Despite the increasingly available types and amounts of omics data, significant knowledge gaps remain, with current approaches to identify and curate missing annot ...

National Academy of Sciences2022

NICEdrug.ch, a workflow for rational drug design and systems-level analysis of drug metabolism

Vassily Hatzimanikatis, Jasmin Maria Hafner, Homa Mohammadi Peyhani, Noushin Hadadi, Anush Chiappino-Pepe

The discovery of a drug requires over a decade of intensive research and financial investments – and still has a high risk of failure. To reduce this burden, we developed the NICEdrug.ch resource, which incorporates 250,000 bioactive molecules, and studied ...

2021

Mechanistic insights into bacterial metabolic reprogramming from omics-integrated genome-scale models

Noushin Hadadi, Vikash Kumar Pandey, Anush Chiappino-Pepe, Merten Morales, Florence Mehl

Understanding the adaptive responses of individual bacterial strains is crucial for microbiome engineering approaches that introduce new functionalities into complex microbiomes, such as xenobiotic compound metabolism for soil bioremediation. Adaptation re ...

NATURE PUBLISHING GROUP2020

Enhanced flux prediction by integrating relative expression and relative metabolite abundance into thermodynamically consistent metabolic models

Vassily Hatzimanikatis, Noushin Hadadi, Vikash Kumar Pandey

The ever-increasing availability of transcriptomic and metabolomic data can be used to deeply analyze and make ever-expanding predictions about biological processes, as changes in the reaction fluxes through genome-wide pathways can now be tracked. Current ...

2019

Enzyme annotation for orphan and novel reactions using knowledge of substrate reactive sites

Vassily Hatzimanikatis, Ljubisa Miskovic, Noushin Hadadi, Marianne Seijo

Thousands of biochemical reactions with characterized activities are “orphan,” meaning they cannot be assigned to a specific enzyme, leaving gaps in metabolic pathways. Novel reactions predicted by pathway-generation tools also lack associated sequences, l ...

National Academy of Sciences2019

Discovery and Evaluation of Biosynthetic Pathways for the Production of Five Methyl Ethyl Ketone Precursors

Vassily Hatzimanikatis, Milenko Tokic, Ljubisa Miskovic, Meriç Ataman, Noushin Hadadi

The limited supply of fossil fuels and the establishment of new environmental policies shifted research in industry and academia towards sustainable production of the 2nd generation of biofuels, with Methyl Ethyl Ketone (MEK) being one promising fuel candi ...

2018

Exploring biochemical pathways for mono-ethylene glycol (MEG) synthesis from synthesis gas

Vassily Hatzimanikatis, Meriç Ataman, Noushin Hadadi

Mono-ethylene glycol (MEG) is an important petrochemical with widespread use in numerous consumer products. The current industrial MEG-production process relies on non-renewable fossil fuel-based feedstocks, such as petroleum, natural gas, and naphtha; hen ...

Academic Press Inc Elsevier Science2017

Reconstruction of biological pathways and metabolic networks from in silico labeled metabolites

Vassily Hatzimanikatis, Jasmin Maria Hafner, Noushin Hadadi, Keng Cher Soh

Reaction atom mappings track the positional changes of all of the atoms between the substrates and the products as they undergo the biochemical transformation. However, information on atom transitions in the context of metabolic pathways is not widely avai ...

Wiley-V C H Verlag Gmbh2017

ATLAS of Biochemistry: A Repository of All Possible Biochemical Reactions for Synthetic Biology and Metabolic Engineering Studies

Vassily Hatzimanikatis, Jasmin Maria Hafner, Noushin Hadadi, Adrian Shajkofci, Aikaterini Zisaki

Because the complexity of metabolism cannot be intuitively understood or analyzed, computational methods are indispensable for studying biochemistry and deepening our understanding of cellular metabolism to promote new discoveries. We used the computationa ...

Amer Chemical Soc2016

Molecular thermodynamics of metabolism: hydration quantities and the equation-of-state approach

Vassily Hatzimanikatis, Meriç Ataman, Noushin Hadadi

The present work is part of a series of papers aiming at a thorough understanding of the thermodynamics of metabolism over a broad range of external conditions. The focus here is on the systematic study of solvation/hydration of a variety of fluids via an ...

Royal Soc Chemistry2016